From 5810a853b0370d09a3f3eb9fc80e8e90bfe8c791 Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Tue, 18 Aug 2015 13:58:30 -0400 Subject: [PATCH 01/46] Move manual_builds.txt to manual_builds.txt.sample to allow for customization --- .gitignore | 1 + scripts/common_startup.sh | 1 + .../shared/ucsc/{manual_builds.txt => manual_builds.txt.sample} | 0 3 files changed, 2 insertions(+) rename tool-data/shared/ucsc/{manual_builds.txt => manual_builds.txt.sample} (100%) diff --git a/.gitignore b/.gitignore index e43721a088c..1bb752fda18 100644 --- a/.gitignore +++ b/.gitignore @@ -76,6 +76,7 @@ tool-data/shared/igv/igv_build_sites.txt tool-data/shared/rviewer/rviewer_build_sites.txt tool-data/shared/ncbi/builds.txt tool-data/shared/ucsc/builds.txt +tool-data/shared/ucsc/manual_builds.txt tool-data/shared/ensembl/builds.txt tool-data/shared/ucsc/publicbuilds.txt tool-data/shared/ucsc/ucsc_build_sites.txt diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh index 34c7e261500..a0ed759db95 100755 --- a/scripts/common_startup.sh +++ b/scripts/common_startup.sh @@ -16,6 +16,7 @@ SAMPLES=" config/shed_data_manager_conf.xml.sample lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample tool-data/shared/ucsc/builds.txt.sample + tool-data/shared/ucsc/manual_builds.txt.sample tool-data/shared/ucsc/ucsc_build_sites.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample diff --git a/tool-data/shared/ucsc/manual_builds.txt b/tool-data/shared/ucsc/manual_builds.txt.sample similarity index 100% rename from tool-data/shared/ucsc/manual_builds.txt rename to tool-data/shared/ucsc/manual_builds.txt.sample From ef23abc6df1dfc1b5ca10d380c2e7a840862c76a Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 18 Sep 2015 15:42:07 +0100 Subject: [PATCH 02/46] WIP: Improved state tracking of HDCA in history panel. For tools which dynamically discover datasets for an output collection, keep the collection yellow until the structure of the HDCA has been fully defined. HDCAs still have the problem that they will always be green even if datasets contained within are in error, running, or queued states - but at least the structure is now reflected in the color. --- client/galaxy/scripts/mvc/collection/collection-model.js | 8 +++++--- client/galaxy/scripts/mvc/history/hdca-li.js | 2 +- lib/galaxy/model/__init__.py | 3 +++ static/maps/mvc/collection/collection-model.js.map | 2 +- static/maps/mvc/history/hdca-li.js.map | 2 +- static/scripts/mvc/collection/collection-model.js | 2 +- static/scripts/mvc/history/hdca-li.js | 2 +- test/api/test_dataset_collections.py | 1 + 8 files changed, 14 insertions(+), 8 deletions(-) diff --git a/client/galaxy/scripts/mvc/collection/collection-model.js b/client/galaxy/scripts/mvc/collection/collection-model.js index 844309f6e6e..49da237372c 100644 --- a/client/galaxy/scripts/mvc/collection/collection-model.js +++ b/client/galaxy/scripts/mvc/collection/collection-model.js @@ -241,10 +241,12 @@ var DatasetCollection = Backbone.Model return json; }, - /** is the collection done with updates and ready to be used? (finished running, etc.) */ + /** Is this collection in a 'ready' state no processing (for the collection) is left + * to do on the server. + */ inReadyState : function(){ -//TODO: state currenly unimplemented for collections - return true; + var populated = this.get( 'populated' ); + return ( this.isDeletedOrPurged() || populated ); }, //TODO:?? the following are the same interface as DatasetAssociation - can we combine? diff --git a/client/galaxy/scripts/mvc/history/hdca-li.js b/client/galaxy/scripts/mvc/history/hdca-li.js index ee633d82e87..c98b5b99527 100644 --- a/client/galaxy/scripts/mvc/history/hdca-li.js +++ b/client/galaxy/scripts/mvc/history/hdca-li.js @@ -46,7 +46,7 @@ var HDCAListItemView = _super.extend( _swapNewRender : function( $newRender ){ _super.prototype._swapNewRender.call( this, $newRender ); //TODO: model currently has no state - var state = this.model.get( 'state' ) || STATES.OK; + var state = !this.model.get( 'populated' ) ? STATES.RUNNING : STATES.OK; //if( this.model.has( 'state' ) ){ this.$el.addClass( 'state-' + state ); //} diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 4811890336f..37a292ea510 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3047,6 +3047,9 @@ class DatasetCollectionInstance( object, HasName ): id=self.id, name=self.name, collection_type=self.collection.collection_type, + populated=self.collection.populated, + populated_state=self.collection.populated_state, + populated_state_message=self.collection.populated_state_message, type="collection", # contents type (distinguished from file or folder (in case of library)) ) diff --git a/static/maps/mvc/collection/collection-model.js.map b/static/maps/mvc/collection/collection-model.js.map index 512f3e27839..534ce4c9de0 100644 --- a/static/maps/mvc/collection/collection-model.js.map +++ b/static/maps/mvc/collection/collection-model.js.map @@ -1 +1 @@ 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a=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+a.join(",")+")"}}),i=h.extend({collectionClass:g,initialize:function(a,b){this.debug(this+"(ListDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),j=i.extend({initialize:function(a,b){this.debug(this+"(PairDatasetCollection).initialize:",a,b),i.prototype.initialize.call(this,a,b)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),k=h.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",a,")"].join("")}})),l=e.extend({model:k,initialize:function(a,b){this.debug(this+"(NestedDCDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=j.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedPairDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",a,")"].join("")}})),n=l.extend({model:m,initialize:function(a,b){this.debug(this+"(NestedPairDCDCECollection).initialize:",a,b),l.prototype.initialize.call(this,a,b)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),o=h.extend({collectionClass:n,initialize:function(a,b){this.debug(this+"(ListPairedDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:i,PairDatasetCollection:j,ListPairedDatasetCollection:o}}); //# sourceMappingURL=../../../maps/mvc/collection/collection-model.js.map \ No newline at end of file diff --git a/static/scripts/mvc/history/hdca-li.js b/static/scripts/mvc/history/hdca-li.js index aa10e9096d2..422c9f9df06 100644 --- a/static/scripts/mvc/history/hdca-li.js +++ b/static/scripts/mvc/history/hdca-li.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["visible"])&&this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("state")||a.OK;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'
',e("This collection has been hidden"),"
","<% } %>"],"collection")}),b=d.wrapTemplate(['
','','
','<%- collection.hid %> ','<%- collection.name %>',"
",'
',"
"],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}}); +define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["visible"])&&this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("populated")?a.OK:a.RUNNING;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'
',e("This collection has been hidden"),"
","<% } %>"],"collection")}),b=d.wrapTemplate(['
','','
','<%- collection.hid %> ','<%- collection.name %>',"
",'
',"
"],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}}); //# sourceMappingURL=../../../maps/mvc/history/hdca-li.js.map \ No newline at end of file diff --git a/test/api/test_dataset_collections.py b/test/api/test_dataset_collections.py index 6993d81b305..2e298fe7698 100644 --- a/test/api/test_dataset_collections.py +++ b/test/api/test_dataset_collections.py @@ -87,6 +87,7 @@ class DatasetCollectionApiTestCase( api.ApiTestCase ): pair_1_object = pair_1_element[ "object" ] self._assert_has_keys( pair_1_object, "collection_type", "elements" ) self.assertEquals( pair_1_object[ "collection_type" ], "paired" ) + self.assertEquals( pair_1_object[ "populated" ], True ) pair_elements = pair_1_object[ "elements" ] assert len( pair_elements ) == 2 pair_1_element_1 = pair_elements[ 0 ] From 98f6dcc4dea061db7c04fbe8e2cd86898d10343b Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Fri, 18 Sep 2015 17:03:54 -0400 Subject: [PATCH 03/46] Render HDCAs when their models change --- client/galaxy/scripts/mvc/history/hdca-li.js | 6 ++---- static/maps/mvc/history/hdca-li.js.map | 2 +- static/scripts/mvc/history/hdca-li.js | 2 +- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/client/galaxy/scripts/mvc/history/hdca-li.js b/client/galaxy/scripts/mvc/history/hdca-li.js index c98b5b99527..b2b9977ef4e 100644 --- a/client/galaxy/scripts/mvc/history/hdca-li.js +++ b/client/galaxy/scripts/mvc/history/hdca-li.js @@ -21,11 +21,9 @@ var HDCAListItemView = _super.extend( /** event listeners */ _setUpListeners : function(){ _super.prototype._setUpListeners.call( this ); - // re-rendering on deletion + this.model.on( 'change', function( model, options ){ - if( _.isEqual( _.keys( model.changed ), [ 'visible' ] ) ){ - this.render(); - } + this.render(); }, this ); }, diff --git a/static/maps/mvc/history/hdca-li.js.map b/static/maps/mvc/history/hdca-li.js.map index 083d56fab03..aa95fa04548 100644 --- a/static/maps/mvc/history/hdca-li.js.map +++ b/static/maps/mvc/history/hdca-li.js.map @@ -1 +1 @@ -{"version":3,"file":"hdca-li.js","sources":["../../../src/mvc/history/hdca-li.js"],"names":["define","STATES","DC_LI","DC_PANEL","BASE_MVC","_l","_super","DCListItemView","HDCAListItemView","extend","className","prototype","_setUpListeners","call","this","model","on","_","isEqual","keys","changed","render","_getFoldoutPanelClass","get","ListCollectionPanel","PairCollectionPanel","ListOfPairsCollectionPanel","TypeError","_swapNewRender","$newRender","state","OK","RUNNING","$el","addClass","toString","modelString","templates","warnings","hidden","wrapTemplate","titleBarTemplate","titleBar"],"mappings":"AAAAA,QACI,qBACA,+BACA,kCACA,eACA,sBACD,SAAUC,EAAQC,EAAOC,EAAUC,EAAUC,GAGhD,GAAIC,GAASJ,EAAMK,eAGfC,EAAmBF,EAAOG,QAM1BC,UAAcJ,EAAOK,UAAUD,UAAY,mBAG3CE,gBAAkB,WACdN,EAAOK,UAAUC,gBAAgBC,KAAMC,MAEvCA,KAAKC,MAAMC,GAAI,SAAU,SAAUD,GAC3BE,EAAEC,QAASD,EAAEE,KAAMJ,EAAMK,UAAa,aACtCN,KAAKO,UAEVP,OAIPQ,sBAAwB,WACpB,OAAQR,KAAKC,MAAMQ,IAAK,oBACpB,IAAK,OACD,MAAOpB,GAASqB,mBACpB,KAAK,SACD,MAAOrB,GAASsB,mBACpB,KAAK,cACD,MAAOtB,GAASuB,2BAExB,KAAM,IAAIC,WAAW,2BAA6Bb,KAAKC,MAAMQ,IAAK,qBAItEK,eAAiB,SAAUC,GACvBvB,EAAOK,UAAUiB,eAAef,KAAMC,KAAMe,EAE5C,IAAIC,GAAShB,KAAKC,MAAMQ,IAAK,aAAiCtB,EAAO8B,GAAxB9B,EAAO+B,OAIpD,OAFAlB,MAAKmB,IAAIC,SAAU,SAAWJ,GAEvBhB,KAAKmB,KAKhBE,SAAW,WACP,GAAIC,GAAgBtB,KAAW,MAAIA,KAAKC,MAAQ,GAAK,YACrD,OAAO,oBAAsBqB,EAAc,MAwC/C,OAnCJ5B,GAAiBG,UAAU0B,UAAa,WAEpC,GAAIC,GAAWrB,EAAER,UAAYH,EAAOK,UAAU0B,UAAUC,UACpDC,OAASnC,EAASoC,cAEd,mCACI,+CACInC,EAAI,mCACR,SACJ,WACD,gBAIHoC,EAAmBrC,EAASoC,cAE5B,6CACI,mCACA,sBAEI,kDACA,mDACJ,SACA,+BACJ,UACD,aAEH,OAAOvB,GAAER,UAAYH,EAAOK,UAAU0B,WAClCC,SAAWA,EACXI,SAAWD,QAOXjC,iBAAmBA"} \ No newline at end of file +{"version":3,"file":"hdca-li.js","sources":["../../../src/mvc/history/hdca-li.js"],"names":["define","STATES","DC_LI","DC_PANEL","BASE_MVC","_l","_super","DCListItemView","HDCAListItemView","extend","className","prototype","_setUpListeners","call","this","model","on","render","_getFoldoutPanelClass","get","ListCollectionPanel","PairCollectionPanel","ListOfPairsCollectionPanel","TypeError","_swapNewRender","$newRender","state","OK","RUNNING","$el","addClass","toString","modelString","templates","warnings","_","hidden","wrapTemplate","titleBarTemplate","titleBar"],"mappings":"AAAAA,QACI,qBACA,+BACA,kCACA,eACA,sBACD,SAAUC,EAAQC,EAAOC,EAAUC,EAAUC,GAGhD,GAAIC,GAASJ,EAAMK,eAGfC,EAAmBF,EAAOG,QAM1BC,UAAcJ,EAAOK,UAAUD,UAAY,mBAG3CE,gBAAkB,WACdN,EAAOK,UAAUC,gBAAgBC,KAAMC,MAEvCA,KAAKC,MAAMC,GAAI,SAAU,WACrBF,KAAKG,UACNH,OAIPI,sBAAwB,WACpB,OAAQJ,KAAKC,MAAMI,IAAK,oBACpB,IAAK,OACD,MAAOhB,GAASiB,mBACpB,KAAK,SACD,MAAOjB,GAASkB,mBACpB,KAAK,cACD,MAAOlB,GAASmB,2BAExB,KAAM,IAAIC,WAAW,2BAA6BT,KAAKC,MAAMI,IAAK,qBAItEK,eAAiB,SAAUC,GACvBnB,EAAOK,UAAUa,eAAeX,KAAMC,KAAMW,EAE5C,IAAIC,GAASZ,KAAKC,MAAMI,IAAK,aAAiClB,EAAO0B,GAAxB1B,EAAO2B,OAIpD,OAFAd,MAAKe,IAAIC,SAAU,SAAWJ,GAEvBZ,KAAKe,KAKhBE,SAAW,WACP,GAAIC,GAAgBlB,KAAW,MAAIA,KAAKC,MAAQ,GAAK,YACrD,OAAO,oBAAsBiB,EAAc,MAwC/C,OAnCJxB,GAAiBG,UAAUsB,UAAa,WAEpC,GAAIC,GAAWC,EAAE1B,UAAYH,EAAOK,UAAUsB,UAAUC,UACpDE,OAAShC,EAASiC,cAEd,mCACI,+CACIhC,EAAI,mCACR,SACJ,WACD,gBAIHiC,EAAmBlC,EAASiC,cAE5B,6CACI,mCACA,sBAEI,kDACA,mDACJ,SACA,+BACJ,UACD,aAEH,OAAOF,GAAE1B,UAAYH,EAAOK,UAAUsB,WAClCC,SAAWA,EACXK,SAAWD,QAOX9B,iBAAmBA"} \ No newline at end of file diff --git a/static/scripts/mvc/history/hdca-li.js b/static/scripts/mvc/history/hdca-li.js index 422c9f9df06..05eb43b6674 100644 --- a/static/scripts/mvc/history/hdca-li.js +++ b/static/scripts/mvc/history/hdca-li.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["visible"])&&this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("populated")?a.OK:a.RUNNING;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'
',e("This collection has been hidden"),"
","<% } %>"],"collection")}),b=d.wrapTemplate(['
','','
','<%- collection.hid %> ','<%- collection.name %>',"
",'
',"
"],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}}); +define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(){this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("populated")?a.OK:a.RUNNING;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'
',e("This collection has been hidden"),"
","<% } %>"],"collection")}),b=d.wrapTemplate(['
','','
','<%- collection.hid %> ','<%- collection.name %>',"
",'
',"
"],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}}); //# sourceMappingURL=../../../maps/mvc/history/hdca-li.js.map \ No newline at end of file From b9913d29316de4058197739b2ae4cfed5c5ae2f3 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Mon, 21 Sep 2015 11:53:29 -0400 Subject: [PATCH 04/46] Swap tool form to use Galaxy.modal --- .../scripts/mvc/tools/tools-form-base.js | 10 +- static/maps/mvc/tools/tools-form-base.js.map | 2 +- static/scripts/mvc/tools/tools-form-base.js | 179 +++++++++++++++++- 3 files changed, 184 insertions(+), 7 deletions(-) diff --git a/client/galaxy/scripts/mvc/tools/tools-form-base.js b/client/galaxy/scripts/mvc/tools/tools-form-base.js index d3fa2cd8b0f..43959ab52bb 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -2,8 +2,9 @@ This is the base class of the tool form plugin. This class is e.g. inherited by the regular and the workflow tool form. */ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', - 'mvc/tools/tools-template', 'mvc/citation/citation-model', 'mvc/citation/citation-view'], - function(Utils, Deferred, Ui, Form, ToolTemplate, CitationModel, CitationView) { + 'mvc/tools/tools-template', 'mvc/citation/citation-model', 'mvc/citation/citation-view', + 'mvc/ui/ui-modal'], + function(Utils, Deferred, Ui, Form, ToolTemplate, CitationModel, CitationView, Modal) { // create form view return Backbone.View.extend({ @@ -11,6 +12,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', initialize: function(options) { this.options = Utils.merge(options, {}); this.setElement('
'); + this.modal = Galaxy.modal; // create deferred processing queue handler // this handler reduces the number of requests to the api by filtering redundant requests @@ -117,12 +119,12 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', // show error var error_message = response.error || 'Uncaught error.'; - self.form.modal.show({ + self.modal.show({ title : 'Tool cannot be executed', body : error_message, buttons : { 'Close' : function() { - self.form.modal.hide(); + self.modal.hide(); } } }); diff --git a/static/maps/mvc/tools/tools-form-base.js.map b/static/maps/mvc/tools/tools-form-base.js.map index a79eda9b999..88a72130cf2 100644 --- a/static/maps/mvc/tools/tools-form-base.js.map +++ b/static/maps/mvc/tools/tools-form-base.js.map @@ -1 +1 @@ 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"),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var d=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)e=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var e=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)e+="dataset_id="+b.dataset_id;else{e+="tool_version="+b.version+"&";var f=top.location.href,g=f.indexOf("?");-1!=f.indexOf("tool_id=")&&-1!==g&&(e+=f.slice(g+1))}}var h=this.deferred.register();a.request({type:"GET",url:e,success:function(a){d._buildForm(a.tool_model||a),!c&&d.form.message.update({status:"success",message:"Now you are using '"+d.options.name+"' version "+d.options.version+".",persistent:!1}),d.deferred.done(h)},error:function(a){d.deferred.done(h);var b=a.error||"Uncaught error.";d.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){d.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),c.deferred.done(f)},error:function(a){c.deferred.done(f)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); -//# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map \ No newline at end of file +define([ "utils/utils", "utils/deferred", "mvc/ui/ui-misc", "mvc/form/form-view", "mvc/tools/tools-template", "mvc/citation/citation-model", "mvc/citation/citation-view", "mvc/ui/ui-modal" ], function(a, b, c, d, e, f, g) { + return Backbone.View.extend({ + initialize: function(c) { + this.options = a.merge(c, {}), this.setElement("
"), this.modal = Galaxy.modal, + this.deferred = new b(), c.inputs ? this._buildForm(c) : this._buildModel(c, !0); + }, + _buildForm: function(b) { + var c = this; + this.options = a.merge(b, this.options), this.options = a.merge({ + icon: "fa-wrench", + title: "" + b.name + " " + b.description + " (Galaxy Tool Version " + b.version + ")", + operations: this._operations(), + onchange: function() { + c.deferred.reset(), c.deferred.execute(function() { + c._updateModel(); + }); + } + }, this.options), this.form = new d(this.options), this._footer(), this.$el.empty(), + this.$el.append(this.form.$el); + }, + _buildModel: function(b, c) { + var d = this; + if (this.options.id = b.id, this.options.version = b.version, b.job_id) e = Galaxy.root + "api/jobs/" + b.job_id + "/build_for_rerun"; else { + var e = Galaxy.root + "api/tools/" + b.id + "/build?"; + if (b.dataset_id) e += "dataset_id=" + b.dataset_id; else { + e += "tool_version=" + b.version + "&"; + var f = top.location.href, g = f.indexOf("?"); + -1 != f.indexOf("tool_id=") && -1 !== g && (e += f.slice(g + 1)); + } + } + var h = this.deferred.register(); + a.request({ + type: "GET", + url: e, + success: function(a) { + d._buildForm(a.tool_model || a), !c && d.form.message.update({ + status: "success", + message: "Now you are using '" + d.options.name + "' version " + d.options.version + ".", + persistent: !1 + }), d.deferred.done(h), console.debug("tools-form::initialize() - Initial tool model ready."), + console.debug(a); + }, + error: function(a) { + d.deferred.done(h), console.debug("tools-form::initialize() - Initial tool model request failed."), + console.debug(a); + var b = a.error || "Uncaught error."; + d.modal.show({ + title: "Tool cannot be executed", + body: b, + buttons: { + Close: function() { + d.modal.hide(); + } + } + }); + } + }); + }, + _updateModel: function() { + var b = this.options.update_url || Galaxy.root + "api/tools/" + this.options.id + "/build", c = this, d = this.form, e = { + tool_id: this.options.id, + tool_version: this.options.version, + inputs: $.extend(!0, {}, c.form.data.create()) + }; + d.wait(!0); + var f = this.deferred.register(); + console.debug("tools-form-base::_updateModel() - Sending current state (see below)."), + console.debug(e), a.request({ + type: "POST", + url: b, + data: e, + success: function(a) { + c.form.update(a.tool_model || a), c.options.update && c.options.update(a), d.wait(!1), + console.debug("tools-form-base::_updateModel() - Received new model (see below)."), + console.debug(a), c.deferred.done(f); + }, + error: function(a) { + c.deferred.done(f), console.debug("tools-form-base::_updateModel() - Refresh request failed."), + console.debug(a); + } + }); + }, + _operations: function() { + var a = this, b = this.options, d = new c.ButtonMenu({ + icon: "fa-cubes", + title: !b.narrow && "Versions" || null, + tooltip: "Select another tool version" + }); + if (!b.is_workflow && b.versions && b.versions.length > 1) for (var f in b.versions) { + var g = b.versions[f]; + g != b.version && d.addMenu({ + title: "Switch to " + g, + version: g, + icon: "fa-cube", + onclick: function() { + var c = b.id.replace(b.version, this.version), d = this.version; + a.deferred.reset(), a.deferred.execute(function() { + a._buildModel({ + id: c, + version: d + }); + }); + } + }); + } else d.$el.hide(); + var h = new c.ButtonMenu({ + icon: "fa-caret-down", + title: !b.narrow && "Options" || null, + tooltip: "View available options" + }); + return b.biostar_url && (h.addMenu({ + icon: "fa-question-circle", + title: "Question?", + tooltip: "Ask a question about this tool (Biostar)", + onclick: function() { + window.open(b.biostar_url + "/p/new/post/"); + } + }), h.addMenu({ + icon: "fa-search", + title: "Search", + tooltip: "Search help for this tool (Biostar)", + onclick: function() { + window.open(b.biostar_url + "/local/search/page/?q=" + b.name); + } + })), h.addMenu({ + icon: "fa-share", + title: "Share", + tooltip: "Share this tool", + onclick: function() { + prompt("Copy to clipboard: Ctrl+C, Enter", window.location.origin + Galaxy.root + "root?tool_id=" + b.id); + } + }), Galaxy.user && Galaxy.user.get("is_admin") && h.addMenu({ + icon: "fa-download", + title: "Download", + tooltip: "Download this tool", + onclick: function() { + window.location.href = Galaxy.root + "api/tools/" + b.id + "/download"; + } + }), b.requirements && b.requirements.length > 0 && h.addMenu({ + icon: "fa-info-circle", + title: "Requirements", + tooltip: "Display tool requirements", + onclick: function() { + this.visible ? (this.visible = !1, a.form.message.update({ + message: "" + })) : (this.visible = !0, a.form.message.update({ + persistent: !0, + message: e.requirements(b), + status: "info" + })); + } + }), b.sharable_url && h.addMenu({ + icon: "fa-external-link", + title: "See in Tool Shed", + tooltip: "Access the repository", + onclick: function() { + window.open(b.sharable_url); + } + }), { + menu: h, + versions: d + }; + }, + _footer: function() { + var a = this.options; + if ("" != a.help && this.form.$el.append(e.help(a)), a.citations) { + var b = $("
"), c = new f.ToolCitationCollection(); + c.tool_id = a.id; + var d = new g.CitationListView({ + el: b, + collection: c + }); + d.render(), c.fetch(), this.form.$el.append(b); + } + } + }); +}); \ No newline at end of file From 83bd9dd541079f0571b90044e1a64d8318377039 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Mon, 21 Sep 2015 12:01:44 -0400 Subject: [PATCH 05/46] repack without --develop --- static/maps/mvc/tools/tools-form-base.js.map | 2 +- static/scripts/mvc/tools/tools-form-base.js | 179 +------------------ 2 files changed, 3 insertions(+), 178 deletions(-) diff --git a/static/maps/mvc/tools/tools-form-base.js.map b/static/maps/mvc/tools/tools-form-base.js.map index 88a72130cf2..2b4524a0e41 100644 --- a/static/maps/mvc/tools/tools-form-base.js.map +++ b/static/maps/mvc/tools/tools-form-base.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-form-base.js b/static/scripts/mvc/tools/tools-form-base.js index be0c8292ed4..6c76174b8cd 100644 --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -1,177 +1,2 @@ -define([ "utils/utils", "utils/deferred", "mvc/ui/ui-misc", "mvc/form/form-view", "mvc/tools/tools-template", "mvc/citation/citation-model", "mvc/citation/citation-view", "mvc/ui/ui-modal" ], function(a, b, c, d, e, f, g) { - return Backbone.View.extend({ - initialize: function(c) { - this.options = a.merge(c, {}), this.setElement("
"), this.modal = Galaxy.modal, - this.deferred = new b(), c.inputs ? this._buildForm(c) : this._buildModel(c, !0); - }, - _buildForm: function(b) { - var c = this; - this.options = a.merge(b, this.options), this.options = a.merge({ - icon: "fa-wrench", - title: "" + b.name + " " + b.description + " (Galaxy Tool Version " + b.version + ")", - operations: this._operations(), - onchange: function() { - c.deferred.reset(), c.deferred.execute(function() { - c._updateModel(); - }); - } - }, this.options), this.form = new d(this.options), this._footer(), this.$el.empty(), - this.$el.append(this.form.$el); - }, - _buildModel: function(b, c) { - var d = this; - if (this.options.id = b.id, this.options.version = b.version, b.job_id) e = Galaxy.root + "api/jobs/" + b.job_id + "/build_for_rerun"; else { - var e = Galaxy.root + "api/tools/" + b.id + "/build?"; - if (b.dataset_id) e += "dataset_id=" + b.dataset_id; else { - e += "tool_version=" + b.version + "&"; - var f = top.location.href, g = f.indexOf("?"); - -1 != f.indexOf("tool_id=") && -1 !== g && (e += f.slice(g + 1)); - } - } - var h = this.deferred.register(); - a.request({ - type: "GET", - url: e, - success: function(a) { - d._buildForm(a.tool_model || a), !c && d.form.message.update({ - status: "success", - message: "Now you are using '" + d.options.name + "' version " + d.options.version + ".", - persistent: !1 - }), d.deferred.done(h), console.debug("tools-form::initialize() - Initial tool model ready."), - console.debug(a); - }, - error: function(a) { - d.deferred.done(h), console.debug("tools-form::initialize() - Initial tool model request failed."), - console.debug(a); - var b = a.error || "Uncaught error."; - d.modal.show({ - title: "Tool cannot be executed", - body: b, - buttons: { - Close: function() { - d.modal.hide(); - } - } - }); - } - }); - }, - _updateModel: function() { - var b = this.options.update_url || Galaxy.root + "api/tools/" + this.options.id + "/build", c = this, d = this.form, e = { - tool_id: this.options.id, - tool_version: this.options.version, - inputs: $.extend(!0, {}, c.form.data.create()) - }; - d.wait(!0); - var f = this.deferred.register(); - console.debug("tools-form-base::_updateModel() - Sending current state (see below)."), - console.debug(e), a.request({ - type: "POST", - url: b, - data: e, - success: function(a) { - c.form.update(a.tool_model || a), c.options.update && c.options.update(a), d.wait(!1), - console.debug("tools-form-base::_updateModel() - Received new model (see below)."), - console.debug(a), c.deferred.done(f); - }, - error: function(a) { - c.deferred.done(f), console.debug("tools-form-base::_updateModel() - Refresh request failed."), - console.debug(a); - } - }); - }, - _operations: function() { - var a = this, b = this.options, d = new c.ButtonMenu({ - icon: "fa-cubes", - title: !b.narrow && "Versions" || null, - tooltip: "Select another tool version" - }); - if (!b.is_workflow && b.versions && b.versions.length > 1) for (var f in b.versions) { - var g = b.versions[f]; - g != b.version && d.addMenu({ - title: "Switch to " + g, - version: g, - icon: "fa-cube", - onclick: function() { - var c = b.id.replace(b.version, this.version), d = this.version; - a.deferred.reset(), a.deferred.execute(function() { - a._buildModel({ - id: c, - version: d - }); - }); - } - }); - } else d.$el.hide(); - var h = new c.ButtonMenu({ - icon: "fa-caret-down", - title: !b.narrow && "Options" || null, - tooltip: "View available options" - }); - return b.biostar_url && (h.addMenu({ - icon: "fa-question-circle", - title: "Question?", - tooltip: "Ask a question about this tool (Biostar)", - onclick: function() { - window.open(b.biostar_url + "/p/new/post/"); - } - }), h.addMenu({ - icon: "fa-search", - title: "Search", - tooltip: "Search help for this tool (Biostar)", - onclick: function() { - window.open(b.biostar_url + "/local/search/page/?q=" + b.name); - } - })), h.addMenu({ - icon: "fa-share", - title: "Share", - tooltip: "Share this tool", - onclick: function() { - prompt("Copy to clipboard: Ctrl+C, Enter", window.location.origin + Galaxy.root + "root?tool_id=" + b.id); - } - }), Galaxy.user && Galaxy.user.get("is_admin") && h.addMenu({ - icon: "fa-download", - title: "Download", - tooltip: "Download this tool", - onclick: function() { - window.location.href = Galaxy.root + "api/tools/" + b.id + "/download"; - } - }), b.requirements && b.requirements.length > 0 && h.addMenu({ - icon: "fa-info-circle", - title: "Requirements", - tooltip: "Display tool requirements", - onclick: function() { - this.visible ? (this.visible = !1, a.form.message.update({ - message: "" - })) : (this.visible = !0, a.form.message.update({ - persistent: !0, - message: e.requirements(b), - status: "info" - })); - } - }), b.sharable_url && h.addMenu({ - icon: "fa-external-link", - title: "See in Tool Shed", - tooltip: "Access the repository", - onclick: function() { - window.open(b.sharable_url); - } - }), { - menu: h, - versions: d - }; - }, - _footer: function() { - var a = this.options; - if ("" != a.help && this.form.$el.append(e.help(a)), a.citations) { - var b = $("
"), c = new f.ToolCitationCollection(); - c.tool_id = a.id; - var d = new g.CitationListView({ - el: b, - collection: c - }); - d.render(), c.fetch(), this.form.$el.append(b); - } - } - }); -}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view","mvc/ui/ui-modal"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("
"),this.modal=Galaxy.modal,this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var d=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)e=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var e=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)e+="dataset_id="+b.dataset_id;else{e+="tool_version="+b.version+"&";var f=top.location.href,g=f.indexOf("?");-1!=f.indexOf("tool_id=")&&-1!==g&&(e+=f.slice(g+1))}}var h=this.deferred.register();a.request({type:"GET",url:e,success:function(a){d._buildForm(a.tool_model||a),!c&&d.form.message.update({status:"success",message:"Now you are using '"+d.options.name+"' version "+d.options.version+".",persistent:!1}),d.deferred.done(h)},error:function(a){d.deferred.done(h);var b=a.error||"Uncaught error.";d.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){d.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),c.deferred.done(f)},error:function(a){c.deferred.done(f)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); +//# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map \ No newline at end of file From 3d697937c7f9d3aff0178f013692d795c3b73eb6 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 22 Sep 2015 10:33:25 -0400 Subject: [PATCH 06/46] Rerun improvement -- instead of allowing someone to try to rerun the upload tool and showing an error message, just don't provide the option for it in the first place. --- client/galaxy/scripts/mvc/dataset/dataset-li-edit.js | 7 ++++++- lib/galaxy/managers/hdas.py | 9 +++++++++ static/maps/mvc/dataset/dataset-li-edit.js.map | 2 +- static/scripts/mvc/dataset/dataset-li-edit.js | 2 +- 4 files changed, 17 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js index 23a8181f3db..85769323fe2 100644 --- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js @@ -159,11 +159,16 @@ var DatasetListItemEdit = _super.extend( /** Render icon-button to re-run the job that created this dataset. */ _renderRerunButton : function(){ var creating_job = this.model.get('creating_job'); - return faIconButton({ + var rerunnable = this.model.get('rerunnable'); + if (!rerunnable){ + return; + } + else return faIconButton({ title : _l( 'Run this job again' ), href : this.model.urls.rerun, classes : 'rerun-btn', target : this.linkTarget, + disabled : !rerunnable, faIcon : 'fa-refresh', onclick : function(ev) { ev.preventDefault(); diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py index db6e767d442..5165098bbfe 100644 --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -280,6 +280,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize 'peek', 'creating_job', + 'rerunnable', 'uuid', 'permissions', @@ -328,6 +329,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize 'resubmitted' : lambda i, k, **c: self.hda_manager.has_been_resubmitted( i ), 'creating_job' : self.serialize_creating_job, + 'rerunnable' : self.rerunnable, 'display_apps' : self.serialize_display_apps, 'display_types' : self.serialize_old_display_applications, @@ -439,6 +441,13 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize else: return None + def rerunnable( self, hda, key, **context ): + if hda.creating_job: + tool = self.app.toolbox.get_tool(hda.creating_job.tool_id, hda.creating_job.tool_version) + if tool and tool.is_workflow_compatible: + return True + return False + class HDADeserializer( datasets.DatasetAssociationDeserializer, taggable.TaggableDeserializerMixin, diff --git a/static/maps/mvc/dataset/dataset-li-edit.js.map b/static/maps/mvc/dataset/dataset-li-edit.js.map index 0436d840ee3..26c267ad438 100644 --- a/static/maps/mvc/dataset/dataset-li-edit.js.map +++ b/static/maps/mvc/dataset/dataset-li-edit.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/dataset/dataset-li-edit.js b/static/scripts/mvc/dataset/dataset-li-edit.js index f44b3f96cb1..8bc096ac20f 100644 --- a/static/scripts/mvc/dataset/dataset-li-edit.js +++ b/static/scripts/mvc/dataset/dataset-li-edit.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","mvc/tools/tools-form","utils/localization"],function(a,b,c,d,e,f,g,h){var i=b.DatasetListItemView,j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=i.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:i.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:h("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=h("Cannot edit attributes of datasets removed from disk"):c&&(d.title=h("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=h("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:h(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=i.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=i.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:h("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var a=this.model.get("creating_job");return e({title:h("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(b){b.preventDefault();var c=new g.View({job_id:a});c.deferred.execute(function(){Galaxy.app.display(c.$el)})}})},_renderVisualizationsButton:function(){var a=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||_.isEmpty(a))return null;if(!_.isObject(a[0]))return this.warn("Visualizations have been switched off"),null;var b=$(this.templates.visualizations(a,this));return b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:h("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:h("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(i.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return j.prototype.templates=function(){var a=_.extend({},i.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
',h("An error occurred setting the metadata for this dataset"),'
',h("Set it manually or retry auto-detection"),"","
","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
',h("This dataset has been deleted"),'
',h("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
',h("Permanently remove it from disk"),"","<% } %>","
","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
','','',"",'","
","<% } %>"],"visualizations");return _.extend({},i.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:j}}); +define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","mvc/tools/tools-form","utils/localization"],function(a,b,c,d,e,f,g,h){var i=b.DatasetListItemView,j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=i.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:i.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:h("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=h("Cannot edit attributes of datasets removed from disk"):c&&(d.title=h("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=h("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:h(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=i.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=i.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:h("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var a=this.model.get("creating_job"),b=this.model.get("rerunnable");return b?e({title:h("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,disabled:!b,faIcon:"fa-refresh",onclick:function(b){b.preventDefault();var c=new g.View({job_id:a});c.deferred.execute(function(){Galaxy.app.display(c.$el)})}}):void 0},_renderVisualizationsButton:function(){var a=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||_.isEmpty(a))return null;if(!_.isObject(a[0]))return this.warn("Visualizations have been switched off"),null;var b=$(this.templates.visualizations(a,this));return b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:h("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:h("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(i.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return j.prototype.templates=function(){var a=_.extend({},i.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
',h("An error occurred setting the metadata for this dataset"),'
',h("Set it manually or retry auto-detection"),"","
","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
',h("This dataset has been deleted"),'
',h("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
',h("Permanently remove it from disk"),"","<% } %>","
","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
','','',"",'","
","<% } %>"],"visualizations");return _.extend({},i.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:j}}); //# sourceMappingURL=../../../maps/mvc/dataset/dataset-li-edit.js.map \ No newline at end of file From 19bc49d207a92288dc402900cfa0125b8da45111 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 22 Sep 2015 17:50:29 -0400 Subject: [PATCH 07/46] Binary sniffing; along with the registry forcing case insensitivity through lower() which was implemented a while back, the un/sniffable formats lists should as well. This resolves #753 --- lib/galaxy/datatypes/binary.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 62a72373b29..4a6bdf0756e 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -41,11 +41,11 @@ class Binary( data.Data ): @staticmethod def register_sniffable_binary_format(data_type, ext, type_class): - Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext, "class": type_class}) + Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext.lower(), "class": type_class}) @staticmethod def register_unsniffable_binary_ext(ext): - Binary.unsniffable_binary_formats.append(ext) + Binary.unsniffable_binary_formats.append(ext.lower()) @staticmethod def is_sniffable_binary( filename ): From fe642fe7fa66a53b4fbb1f89e200c10ead7854a6 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 22 Sep 2015 19:48:59 -0400 Subject: [PATCH 08/46] Tweak tool execution to automatically pull detail ids for new hdas on execution success model update so rerun can be immediate. --- client/galaxy/scripts/mvc/tools/tools-jobs.js | 13 +++++++++---- static/maps/mvc/tools/tools-jobs.js.map | 2 +- static/scripts/mvc/tools/tools-jobs.js | 2 +- 3 files changed, 11 insertions(+), 6 deletions(-) diff --git a/client/galaxy/scripts/mvc/tools/tools-jobs.js b/client/galaxy/scripts/mvc/tools/tools-jobs.js index ccd746630bb..34535665f4b 100644 --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -35,7 +35,12 @@ return { success : function(response) { callback && callback(); form.reciept(ToolTemplate.success(response)); - self._refreshHdas(); + // Get hda ids from response, request detailed refresh of these. + var detailIds = []; + response.outputs.forEach(function(e, i, a){ + detailIds.push(e.id); + }); + self._refreshHdas(detailIds); }, error : function(response, response_full) { callback && callback(); @@ -135,11 +140,11 @@ return { /** Refreshes the history panel */ - _refreshHdas: function() { + _refreshHdas: function(detailIds) { if (parent.Galaxy && parent.Galaxy.currHistoryPanel) { - parent.Galaxy.currHistoryPanel.refreshContents(); + parent.Galaxy.currHistoryPanel.refreshContents(detailIds); } } }; -}); \ No newline at end of file +}); diff --git a/static/maps/mvc/tools/tools-jobs.js.map b/static/maps/mvc/tools/tools-jobs.js.map index 70bd5a497f3..dd27789be87 100644 --- a/static/maps/mvc/tools/tools-jobs.js.map +++ b/static/maps/mvc/tools/tools-jobs.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-jobs.js b/static/scripts/mvc/tools/tools-jobs.js index f6926c6c383..89da5ea8c4b 100644 --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}}):void(e&&e())},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+k+" selection(s) while a previous field contains "+d+"."),!1}}}return!0},_refreshHdas:function(){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()}}}); +define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a));var d=[];a.outputs.forEach(function(a){d.push(a.id)}),f._refreshHdas(d)},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}}):void(e&&e())},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+k+" selection(s) while a previous field contains "+d+"."),!1}}}return!0},_refreshHdas:function(a){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents(a)}}}); //# sourceMappingURL=../../../maps/mvc/tools/tools-jobs.js.map \ No newline at end of file From 684be5f6a5c4ac91d6df2c5ec4f1e2866a538965 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 23 Sep 2015 12:02:06 +0100 Subject: [PATCH 09/46] Functional test to verify RData is not decompressed in upload process. --- test/api/helpers.py | 18 +++++++++++++++--- test/api/test_tools.py | 17 ++++++++++++++++- test/base/test_data.py | 2 +- test/base/twilltestcase.py | 2 +- 4 files changed, 33 insertions(+), 6 deletions(-) diff --git a/test/api/helpers.py b/test/api/helpers.py index dfb07f46776..ebe0d493046 100644 --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -100,10 +100,14 @@ class BaseDatasetPopulator( object ): file_type = kwds.get( "file_type", 'txt' ) upload_params = { 'files_0|NAME': name, - 'files_0|url_paste': content, 'dbkey': dbkey, 'file_type': file_type, } + if isinstance( content, file ): + upload_params[ "files_0|file_data"] = content + else: + upload_params[ 'files_0|url_paste' ] = content + if "to_posix_lines" in kwds: upload_params[ "files_0|to_posix_lines"] = kwds[ "to_posix_lines" ] if "space_to_tab" in kwds: @@ -116,6 +120,10 @@ class BaseDatasetPopulator( object ): ) def run_tool_payload( self, tool_id, inputs, history_id, **kwds ): + if "files_0|file_data" in inputs: + kwds[ "__files" ] = { "files_0|file_data": inputs[ "files_0|file_data" ] } + del inputs[ "files_0|file_data" ] + return dict( tool_id=tool_id, inputs=json.dumps(inputs), @@ -174,8 +182,12 @@ class DatasetPopulator( BaseDatasetPopulator ): def __init__( self, galaxy_interactor ): self.galaxy_interactor = galaxy_interactor - def _post( self, route, data={} ): - return self.galaxy_interactor.post( route, data ) + def _post( self, route, data={}, files=None ): + files = data.get( "__files", None ) + if files is not None: + del data[ "__files" ] + + return self.galaxy_interactor.post( route, data, files=files ) def _get( self, route ): return self.galaxy_interactor.get( route ) diff --git a/test/api/test_tools.py b/test/api/test_tools.py index 74fa95d743c..edf177e3737 100644 --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -5,6 +5,7 @@ from .helpers import DatasetPopulator from .helpers import DatasetCollectionPopulator from .helpers import LibraryPopulator from .helpers import skip_without_tool +from base.test_data import TestDataResolver class ToolsTestCase( api.ApiTestCase ): @@ -109,6 +110,12 @@ class ToolsTestCase( api.ApiTestCase ): result_content = self._upload_and_get_content( table ) self.assertEquals( result_content, table ) + def test_rdata_not_decompressed( self ): + # Prevent regression of https://github.com/galaxyproject/galaxy/issues/753 + rdata_path = TestDataResolver().get_filename("1.RData") + rdata_metadata = self._upload_and_get_details( open(rdata_path, "rb"), file_type="auto" ) + self.assertEquals( rdata_metadata[ "file_ext" ], "rdata" ) + @skip_without_tool( "multi_select" ) def test_multi_select_as_list( self ): history_id = self.dataset_populator.new_history() @@ -1042,12 +1049,20 @@ class ToolsTestCase( api.ApiTestCase ): else: return create_response - def _upload_and_get_content( self, content, **upload_kwds ): + def _upload( self, content, **upload_kwds ): history_id = self.dataset_populator.new_history() new_dataset = self.dataset_populator.new_dataset( history_id, content=content, **upload_kwds ) self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + return history_id, new_dataset + + def _upload_and_get_content( self, content, **upload_kwds ): + history_id, new_dataset = self._upload( content, **upload_kwds ) return self.dataset_populator.get_history_dataset_content( history_id, dataset=new_dataset ) + def _upload_and_get_details( self, content, **upload_kwds ): + history_id, new_dataset = self._upload( content, **upload_kwds ) + return self.dataset_populator.get_history_dataset_details( history_id, dataset=new_dataset ) + def __tool_ids( self ): index = self._get( "tools" ) tools_index = index.json() diff --git a/test/base/test_data.py b/test/base/test_data.py index fa14c8f93fd..6114e342a61 100644 --- a/test/base/test_data.py +++ b/test/base/test_data.py @@ -23,7 +23,7 @@ LIST_SEP = re.compile("\s*,\s*") class TestDataResolver(object): - def __init__(self, env_var, environ=os.environ): + def __init__(self, env_var='GALAXY_TEST_FILE_DIR', environ=os.environ): file_dirs = environ.get(env_var, None) if file_dirs: self.resolvers = map(lambda u: build_resolver(u, environ), LIST_SEP.split(file_dirs)) diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index 88fdae40c6b..fa956559081 100644 --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -50,7 +50,7 @@ class TwillTestCase( unittest.TestCase ): self.host = os.environ.get( 'GALAXY_TEST_HOST' ) self.port = os.environ.get( 'GALAXY_TEST_PORT' ) self.url = "http://%s:%s" % ( self.host, self.port ) - self.test_data_resolver = TestDataResolver( 'GALAXY_TEST_FILE_DIR' ) + self.test_data_resolver = TestDataResolver( ) self.tool_shed_test_file = os.environ.get( 'GALAXY_TOOL_SHED_TEST_FILE', None ) if self.tool_shed_test_file: f = open( self.tool_shed_test_file, 'r' ) From 61fda5f23dce31da353bbee209c8cf260427a400 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 23 Sep 2015 15:10:06 +0100 Subject: [PATCH 10/46] Add missing file from previous commit. --- test-data/1.RData | Bin 0 -> 59 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 test-data/1.RData diff --git a/test-data/1.RData b/test-data/1.RData new file mode 100644 index 0000000000000000000000000000000000000000..8ce4600d934930c86ab6a5ca18aa2b6560779b05 GIT binary patch literal 59 zcmb2|=3oE=X6~X+gGXHtk`fXUk`maG)Y23tw{m(I7;P{pXnNtIaF9LeMtwp Date: Wed, 23 Sep 2015 11:04:20 -0400 Subject: [PATCH 11/46] Backport keyup to change input --- client/galaxy/scripts/mvc/upload/upload-row.js | 2 +- static/maps/mvc/upload/upload-row.js.map | 2 +- static/scripts/mvc/upload/upload-row.js | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/upload/upload-row.js b/client/galaxy/scripts/mvc/upload/upload-row.js index fde0545dd0f..5889d3fec57 100644 --- a/client/galaxy/scripts/mvc/upload/upload-row.js +++ b/client/galaxy/scripts/mvc/upload/upload-row.js @@ -118,7 +118,7 @@ return Backbone.View.extend({ .on('mousedown', function(e) { e.preventDefault(); }); // handle text editing event - it.find('#text-content').on('keyup', function(e) { + it.find('#text-content').on('change input', function(e) { self.model.set('url_paste', $(e.target).val()); self.model.set('file_size', $(e.target).val().length); }); diff --git a/static/maps/mvc/upload/upload-row.js.map b/static/maps/mvc/upload/upload-row.js.map index ed09a46fb9e..4923eeca7ee 100644 --- a/static/maps/mvc/upload/upload-row.js.map +++ b/static/maps/mvc/upload/upload-row.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/upload/upload-row.js b/static/scripts/mvc/upload/upload-row.js index 2f77c021d5b..823daa9ad71 100644 --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(a,b,c,d,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(a,c){this.app=a;var f=this;this.model=new b.Model(c),this.setElement(this._template(c));var g=this.$el;this.settings=new d.View({title:"Upload configuration",container:g.find("#settings"),placement:"bottom"});var h=this.app.select_genome.value();this.select_genome=new e.View({css:"genome",onchange:function(a){f.model.set("genome",a),f.app.updateGenome(a,!0)},data:f.app.list_genomes,container:g.find("#genome"),value:h}),this.model.set("genome",h);var i=this.app.select_extension.value();this.select_extension=new e.View({css:"extension",onchange:function(a){f.model.set("extension",a),f.app.updateExtension(a,!0)},data:f.app.list_extensions,container:g.find("#extension"),value:i}),this.model.set("extension",i),g.find("#symbol").on("click",function(){f._removeRow()}),g.find("#extension-info").on("click",function(a){f.app.showExtensionInfo({$el:$(a.target),title:f.select_extension.text(),extension:f.select_extension.value()})}).on("mousedown",function(a){a.preventDefault()}),g.find("#settings").on("click",function(){f._showSettings()}).on("mousedown",function(a){a.preventDefault()}),g.find("#text-content").on("keyup",function(a){f.model.set("url_paste",$(a.target).val()),f.model.set("file_size",$(a.target).val().length)}),g.find("#space_to_tabs").on("change",function(a){f.model.set("space_to_tabs",$(a.target).prop("checked"))}),this.model.on("change:percentage",function(){f._refreshPercentage()}),this.model.on("change:status",function(){f._refreshStatus()}),this.model.on("change:info",function(){f._refreshInfo()}),this.model.on("change:genome",function(){f._refreshGenome()}),this.model.on("change:extension",function(){f._refreshExtension()}),this.model.on("change:file_size",function(){f._refreshFileSize()}),this.model.on("remove",function(){f.remove()}),this.app.collection.on("reset",function(){f.remove()})},render:function(){var b=this.model.get("file_name"),c=this.model.get("file_size"),d=this.model.get("file_mode"),e=this.$el;if(e.find("#title").html(b),e.find("#size").html(a.bytesToString(c)),e.find("#mode").removeClass().addClass("mode"),"new"==d){var f=e.find("#text"),g=this.options.padding,h=e.width()-2*g,i=e.height()-g;f.css("width",h+"px"),f.css("top",i+"px"),e.height(i+f.height()+2*g),f.show(),e.find("#mode").addClass("fa fa-pencil")}"local"==d&&e.find("#mode").addClass("fa fa-laptop"),"ftp"==d&&e.find("#mode").addClass("fa fa-code-fork")},remove:function(){this.select_genome.remove(),this.select_extension.remove(),Backbone.View.prototype.remove.apply(this)},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var a=this.model.get("info");a?this.$el.find("#info").html("Failed: "+a).show():this.$el.find("#info").hide()},_refreshPercentage:function(){var a=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:a+"%"}),this.$el.find("#percentage").html(100!=a?a+"%":"Adding to history...")},_refreshStatus:function(){var a=this.$el,b=this.model.get("status"),c=this.status_classes[b],d=this.$el.find("#symbol");d.removeClass(),d.addClass(c),"init"==b?(this.select_genome.enable(),this.select_extension.enable(),a.find("#text-content").attr("disabled",!1),a.find("#space_to_tabs").attr("disabled",!1)):(this.select_genome.disable(),this.select_extension.disable(),a.find("#text-content").attr("disabled",!0),a.find("#space_to_tabs").attr("disabled",!0)),"success"==b&&(a.addClass("success"),a.find("#percentage").html("100%")),"error"==b&&(a.addClass("danger"),a.find(".progress").remove())},_refreshFileSize:function(){var b=this.model.get("file_size");this.$el.find("#size").html(a.bytesToString(b))},_removeRow:function(){var a=this.model.get("status");("init"==a||"success"==a||"error"==a)&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new c(this).$el),this.settings.show())},_template:function(a){return'
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