galaxy-commits January 2015

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248 discussions

[galaxyproject/usegalaxy-playbook] 74c4aa: Run data manager (eventually plural) on test-insta...
by GitHub 20 Jan '15

20 Jan '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 74c4aa6aea0dac83f8fa82d6ccc56b14bed32744 https://github.com/galaxyproject/usegalaxy-playbook/commit/74c4aa6aea0dac83… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-01-19 (Mon, 19 Jan 2015) Changed paths: M galaxy.yml A galaxy_infrastructure.yml A production/host_vars/galaxy-web-01.tacc.utexas.edu.yml A production/host_vars/galaxy-web-02.tacc.utexas.edu.yml M pulsar.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Run data manager (eventually plural) on test-installer. Prep for supervisor improvements on Main

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commit/galaxy-central: martenson: Merged in dannon/galaxy-central/stable (pull request #635)
by commits-noreply＠bitbucket.org 20 Jan '15

20 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f1cd1bec8272/ Changeset: f1cd1bec8272 Branch: stable User: martenson Date: 2015-01-19 20:45:50+00:00 Summary: Merged in dannon/galaxy-central/stable (pull request #635) [STABLE]Bump bioblend to 0.5.2. Affected #: 1 file diff -r 895c3fa76b5f6bf2cae22e26d9a13a3feec09d0a -r f1cd1bec8272617ebe3c2776a629b472db0c1f92 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -34,7 +34,7 @@ amqp = 1.4.5 anyjson = 0.3.3 Beaker = 1.4 -bioblend = 0.4.2 +bioblend = 0.5.2 boto = 2.27.0 decorator = 3.1.2 docutils = 0.7 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Jan '15

20 Jan '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d2270c75d05/ Changeset: 1d2270c75d05 Branch: stable User: dannon Date: 2015-01-15 16:59:20+00:00 Summary: Bump bioblend to 0.5.2. The egg no longer depends on mock, which is sort of a bandaid fix for the startup eggs dependency bug not fetching it correctly. TODO: followup on that bug. Affected #: 1 file diff -r 5e1b2c9da932b46776e56453d1bd2acec5c89760 -r 1d2270c75d05495044100ede7be2368112d024a9 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -34,7 +34,7 @@ amqp = 1.4.5 anyjson = 0.3.3 Beaker = 1.4 -bioblend = 0.4.2 +bioblend = 0.5.2 boto = 2.27.0 decorator = 3.1.2 docutils = 0.7 https://bitbucket.org/galaxy/galaxy-central/commits/f1cd1bec8272/ Changeset: f1cd1bec8272 Branch: stable User: martenson Date: 2015-01-19 20:45:50+00:00 Summary: Merged in dannon/galaxy-central/stable (pull request #635) [STABLE]Bump bioblend to 0.5.2. Affected #: 1 file diff -r 895c3fa76b5f6bf2cae22e26d9a13a3feec09d0a -r f1cd1bec8272617ebe3c2776a629b472db0c1f92 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -34,7 +34,7 @@ amqp = 1.4.5 anyjson = 0.3.3 Beaker = 1.4 -bioblend = 0.4.2 +bioblend = 0.5.2 boto = 2.27.0 decorator = 3.1.2 docutils = 0.7 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] ccfff6: Add the supervisor role as a semi-generalized way ...
by GitHub 20 Jan '15

20 Jan '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ccfff62c59d8f9e98d25b89e2c585dcbda8c5646 https://github.com/galaxyproject/usegalaxy-playbook/commit/ccfff62c59d8f9e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-01-19 (Mon, 19 Jan 2015) Changed paths: M galaxy.yml A roles/supervisor/defaults/main.yml A roles/supervisor/handlers/main.yml A roles/supervisor/tasks/main.yml A roles/supervisor/templates/centos.init.j2 A roles/supervisor/templates/debian.init.j2 A roles/supervisor/templates/redhat.init.j2 A roles/supervisor/templates/supervisord.conf.j2 A roles/supervisor/templates/ubuntu.init.j2 M stage/group_vars/galaxyservers.yml M stage/group_vars/pulsarservers.yml A stage/host_vars/galaxy01.tacc.utexas.edu.yml M stage/inventory M stage/secret_vars/galaxyservers.yml A templates/supervisor/galaxy.conf.j2 A templates/supervisor/galaxy_group.conf.j2 A templates/supervisor/galaxy_impersonate.conf.j2 A templates/supervisor/galaxy_installer.conf.j2 A templates/supervisor/galaxy_reports.conf.j2 Log Message: ----------- Add the supervisor role as a semi-generalized way to install and manage supervisor in a self-contained virtualenv. Manage Test's supervisor configs.

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commit/galaxy-central: natefoo: Update tag latest_2015.01.13 for changeset 0cb6cec4ee57
by commits-noreply＠bitbucket.org 19 Jan '15

19 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/895c3fa76b5f/ Changeset: 895c3fa76b5f Branch: stable User: natefoo Date: 2015-01-19 14:00:26+00:00 Summary: Update tag latest_2015.01.13 for changeset 0cb6cec4ee57 Affected #: 1 file diff -r 0cb6cec4ee575c5c07d845ad249c47e7fba0ae62 -r 895c3fa76b5f6bf2cae22e26d9a13a3feec09d0a .hgtags --- a/.hgtags +++ b/.hgtags @@ -22,4 +22,4 @@ 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -f7235d0ad14fd90b8977e88f68715a7dedc5bab9 latest_2015.01.13 +0cb6cec4ee575c5c07d845ad249c47e7fba0ae62 latest_2015.01.13 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Fix space_to_tab option and LibraryDatasetToolParameter
by commits-noreply＠bitbucket.org 19 Jan '15

19 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/df1ebf696eaa/ Changeset: df1ebf696eaa User: guerler Date: 2015-01-18 21:20:04+00:00 Summary: Fix space_to_tab option and LibraryDatasetToolParameter Affected #: 4 files diff -r 17207774b4b7a601698279c7700fb3bf5449e5be -r df1ebf696eaac7f2885117e0f4f2007b645cf17f client/galaxy/scripts/mvc/upload/upload-view.js --- a/client/galaxy/scripts/mvc/upload/upload-view.js +++ b/client/galaxy/scripts/mvc/upload/upload-view.js @@ -335,8 +335,8 @@ tool_input['dbkey'] = genome; tool_input['file_type'] = extension; tool_input['files_0|type'] = 'upload_dataset'; - tool_input['space_to_tabs'] = space_to_tabs; - tool_input['to_posix_lines'] = to_posix_lines; + tool_input['files_0|space_to_tab'] = space_to_tabs && 'Yes' || null; + tool_input['files_0|to_posix_lines'] = to_posix_lines && 'Yes' || null; // setup data data = {}; diff -r 17207774b4b7a601698279c7700fb3bf5449e5be -r df1ebf696eaac7f2885117e0f4f2007b645cf17f lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2422,7 +2422,7 @@ def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.LibraryField( self.name, value=value, trans=trans ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return None def from_html( self, value, trans, other_values={} ): diff -r 17207774b4b7a601698279c7700fb3bf5449e5be -r df1ebf696eaac7f2885117e0f4f2007b645cf17f static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -335,8 +335,8 @@ tool_input['dbkey'] = genome; tool_input['file_type'] = extension; tool_input['files_0|type'] = 'upload_dataset'; - tool_input['space_to_tabs'] = space_to_tabs; - tool_input['to_posix_lines'] = to_posix_lines; + tool_input['files_0|space_to_tab'] = space_to_tabs && 'Yes' || null; + tool_input['files_0|to_posix_lines'] = to_posix_lines && 'Yes' || null; // setup data data = {}; diff -r 17207774b4b7a601698279c7700fb3bf5449e5be -r df1ebf696eaac7f2885117e0f4f2007b645cf17f static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$(".with-upload-button").append((new e.View(this.ui_button)).$el);var h=this;f.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}}});f.get({url:galaxy_config.root+"api/genomes",success:function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})}});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.show()},500);return}if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$(".with-upload-button").append((new e.View(this.ui_button)).$el);var h=this;f.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}}});f.get({url:galaxy_config.root+"api/genomes",success:function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})}});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.show()},500);return}if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|space_to_tab"]=l&&"Yes"||null;tool_input["files_0|to_posix_lines"]=i&&"Yes"||null;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in guerler/guerler-galaxy-central/stable (pull request #639)
by commits-noreply＠bitbucket.org 18 Jan '15

18 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0cb6cec4ee57/ Changeset: 0cb6cec4ee57 Branch: stable User: dannon Date: 2015-01-18 13:39:43+00:00 Summary: Merged in guerler/guerler-galaxy-central/stable (pull request #639) Fix for LibraryDatasetToolParameter Affected #: 1 file diff -r 94088f742ba9c1c822c22976387fd19384dad4de -r 0cb6cec4ee575c5c07d845ad249c47e7fba0ae62 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2386,7 +2386,7 @@ def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.LibraryField( self.name, value=value, trans=trans ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return None def from_html( self, value, trans, other_values={} ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 18 Jan '15

18 Jan '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/147a588e9774/ Changeset: 147a588e9774 Branch: stable User: guerler Date: 2015-01-15 21:09:24+00:00 Summary: Fix for LibraryDatasetToolParameter Affected #: 1 file diff -r 5e1b2c9da932b46776e56453d1bd2acec5c89760 -r 147a588e97749a289eb25514fb59165671cdc095 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2386,7 +2386,7 @@ def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.LibraryField( self.name, value=value, trans=trans ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return None def from_html( self, value, trans, other_values={} ): https://bitbucket.org/galaxy/galaxy-central/commits/0cb6cec4ee57/ Changeset: 0cb6cec4ee57 Branch: stable User: dannon Date: 2015-01-18 13:39:43+00:00 Summary: Merged in guerler/guerler-galaxy-central/stable (pull request #639) Fix for LibraryDatasetToolParameter Affected #: 1 file diff -r 94088f742ba9c1c822c22976387fd19384dad4de -r 0cb6cec4ee575c5c07d845ad249c47e7fba0ae62 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2386,7 +2386,7 @@ def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.LibraryField( self.name, value=value, trans=trans ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return None def from_html( self, value, trans, other_values={} ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: Include a message where in API actually create jobs.
by commits-noreply＠bitbucket.org 17 Jan '15

17 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/17207774b4b7/ Changeset: 17207774b4b7 User: martenson Date: 2015-01-16 22:33:41+00:00 Summary: Include a message where in API actually create jobs. Affected #: 1 file diff -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 -r 17207774b4b7a601698279c7700fb3bf5449e5be lib/galaxy/webapps/galaxy/api/jobs.py --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -215,7 +215,8 @@ @expose_api def create( self, trans, payload, **kwd ): - raise NotImplementedError() + """ See the create method in tools.py in order to submit a job. """ + raise NotImplementedError( 'Please POST to /api/tools instead.' ) @expose_api def search( self, trans, payload, **kwd ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Update tag latest_2015.01.13 for changeset f7235d0ad14f
by commits-noreply＠bitbucket.org 16 Jan '15

16 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/94088f742ba9/ Changeset: 94088f742ba9 Branch: stable User: natefoo Date: 2015-01-16 14:00:18+00:00 Summary: Update tag latest_2015.01.13 for changeset f7235d0ad14f Affected #: 1 file diff -r f7235d0ad14fd90b8977e88f68715a7dedc5bab9 -r 94088f742ba9c1c822c22976387fd19384dad4de .hgtags --- a/.hgtags +++ b/.hgtags @@ -22,4 +22,4 @@ 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -3b559c4b9399236ae2a76ea1f061fcd660e76ed5 latest_2015.01.13 +f7235d0ad14fd90b8977e88f68715a7dedc5bab9 latest_2015.01.13 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits January 2015