1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5fd196b5d176/ Changeset: 5fd196b5d176 Branch: stable User: jmchilton Date: 2014-04-17 22:02:44 Summary: Merged in dan/galaxy-central-stable-prs/stable (pull request #369) BioStar fixes Affected #: 6 files diff -r a0ccb7e6bfdfe5058561e709a81dee9f26e5c991 -r 5fd196b5d1760d1a8180184f8e5450e0957b37c2 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -329,6 +329,8 @@ self.biostar_url = kwargs.get( 'biostar_url', None ) self.biostar_key_name = kwargs.get( 'biostar_key_name', None ) self.biostar_key = kwargs.get( 'biostar_key', None ) + self.biostar_enable_bug_reports = string_as_bool( kwargs.get( 'biostar_enable_bug_reports', True ) ) + self.biostar_never_authenticate = string_as_bool( kwargs.get( 'biostar_never_authenticate', False ) ) self.pretty_datetime_format = expand_pretty_datetime_format( kwargs.get( 'pretty_datetime_format', '$locale (UTC)' ) ) self.master_api_key = kwargs.get( 'master_api_key', None ) if self.master_api_key == "changethis": # default in sample config file diff -r a0ccb7e6bfdfe5058561e709a81dee9f26e5c991 -r 5fd196b5d1760d1a8180184f8e5450e0957b37c2 lib/galaxy/util/biostar.py --- a/lib/galaxy/util/biostar.py +++ b/lib/galaxy/util/biostar.py @@ -2,6 +2,7 @@ Support for integration with the Biostar application """ +import logging import hmac import urlparse import re @@ -10,9 +11,11 @@ from galaxy.tools.errors import ErrorReporter from . import smart_str +log = logging.getLogger( __name__ ) + _punct_re = re.compile(r'[\t !"#$%&\'()*\-/<=>?@\[\\\]^_`{|},.]+') -DEFAULT_GALAXY_TAG = 'galaxy' +DEFAULT_GALAXY_TAG = '' # Default values for new posts to Biostar DEFAULT_PAYLOAD = { @@ -77,7 +80,10 @@ def populate_tag_payload( payload=None, tool=None ): if payload is None: payload = {} - tag_val = [ DEFAULT_GALAXY_TAG ] + if DEFAULT_GALAXY_TAG: + tag_val = [ DEFAULT_GALAXY_TAG ] + else: + tag_val = [] if tool: tag_val.append( tag_for_tool( tool ) ) payload[ 'tag_val' ] = ','.join( tag_val ) @@ -110,7 +116,10 @@ return galaxy_hostname -def create_cookie( trans, key_name, key, email, age=DEFAULT_BIOSTAR_COOKIE_AGE ): +def create_cookie( trans, key_name, key, email, age=DEFAULT_BIOSTAR_COOKIE_AGE, override_never_authenticate=False ): + if trans.app.config.biostar_never_authenticate and not override_never_authenticate: + log.debug( 'A BioStar link was clicked, but never authenticate has been enabled, so we will not create the login cookie.' ) + return digest = hmac.new( key, email ).hexdigest() value = "%s:%s" % (email, digest) trans.set_cookie( value, name=key_name, path='/', age=age, version='1' ) @@ -122,7 +131,7 @@ def delete_cookie( trans, key_name ): #Set expiration of Cookie to time in past, to cause browser to delete if key_name in trans.request.cookies: - create_cookie( trans, trans.app.config.biostar_key_name, '', '', age=-90 ) + create_cookie( trans, trans.app.config.biostar_key_name, '', '', age=-90, override_never_authenticate=True ) def biostar_logged_in( trans ): if biostar_enabled( trans.app ): @@ -139,6 +148,7 @@ class BiostarErrorReporter( ErrorReporter ): def _send_report( self, user, email=None, message=None, **kwd ): assert biostar_enabled( self.app ), ValueError( "Biostar is not configured for this galaxy instance" ) + assert self.app.config.biostar_enable_bug_reports, ValueError( "Biostar is not configured to allow bug reporting for this galaxy instance" ) assert self._can_access_dataset( user ), Exception( "You are not allowed to access this dataset." ) tool_version_select_field, tools, tool = \ self.app.toolbox.get_tool_components( self.tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True ) diff -r a0ccb7e6bfdfe5058561e709a81dee9f26e5c991 -r 5fd196b5d1760d1a8180184f8e5450e0957b37c2 static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -196,7 +196,7 @@ { tab_help.add({ title : "Galaxy Q&A Site", - content : this.options.biostar_url_redirect, + content : this.options.biostar_url, target : "_blank" }); tab_help.add({ diff -r a0ccb7e6bfdfe5058561e709a81dee9f26e5c991 -r 5fd196b5d1760d1a8180184f8e5450e0957b37c2 static/scripts/packed/galaxy.menu.js --- a/static/scripts/packed/galaxy.menu.js +++ b/static/scripts/packed/galaxy.menu.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var e=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"root/index",title_attribute:"Analysis home view"});this.masthead.append(e);var g={id:"workflow",title:"Workflow",content:"workflow",title_attribute:"Chain tools into workflows"};if(!this.options.user.valid){g.disabled=true}var d=new b.GalaxyMastheadTab(g);this.masthead.append(d);var i=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index",title_attribute:"Access published resources"});i.add({title:"Data Libraries",content:"library/index"});i.add({title:"Data Libraries Beta",content:"library/list",divider:true});i.add({title:"Published Histories",content:"history/list_published"});i.add({title:"Published Workflows",content:"workflow/list_published"});i.add({title:"Published Visualizations",content:"visualization/list_published"});i.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(i);if(this.options.user.requests){var j=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});j.add({title:"Sequencing Requests",content:"requests/index"});j.add({title:"Find Samples",content:"requests/find_samples_index"});j.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(j)}var c={id:"visualization",title:"Visualization",content:"visualization/list",title_attribute:"Visualize datasets"};if(!this.options.user.valid){c.disabled=true}var m=new b.GalaxyMastheadTab(c);if(this.options.user.valid){m.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});m.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"})}this.masthead.append(m);if(this.options.enable_cloud_launch){var f=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});f.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(f)}if(this.options.is_admin_user){var h=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only",title_attribute:"Administer this Galaxy"});this.masthead.append(h)}var l=new b.GalaxyMastheadTab({id:"help",title:"Help",title_attribute:"Support, contact, and community hubs"});if(this.options.biostar_url){l.add({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});l.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}l.add({title:"Support",content:this.options.support_url,target:"_blank"});l.add({title:"Search",content:this.options.search_url,target:"_blank"});l.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});l.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});l.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});l.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(this.options.terms_url){l.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(l);if(!this.options.user.valid){var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only",title_attribute:"Account registration or login"});k.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){k.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(k)}else{var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only",title_attribute:"Account preferences and saved data"});k.add({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){k.add({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{k.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});k.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});k.add({title:"Logout",content:"user/logout",target:"_top",divider:true})}k.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});k.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});k.add({title:"Saved Pages",content:"page/list",target:"_top"});k.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){k.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(k)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var e=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"root/index",title_attribute:"Analysis home view"});this.masthead.append(e);var g={id:"workflow",title:"Workflow",content:"workflow",title_attribute:"Chain tools into workflows"};if(!this.options.user.valid){g.disabled=true}var d=new b.GalaxyMastheadTab(g);this.masthead.append(d);var i=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index",title_attribute:"Access published resources"});i.add({title:"Data Libraries",content:"library/index"});i.add({title:"Data Libraries Beta",content:"library/list",divider:true});i.add({title:"Published Histories",content:"history/list_published"});i.add({title:"Published Workflows",content:"workflow/list_published"});i.add({title:"Published Visualizations",content:"visualization/list_published"});i.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(i);if(this.options.user.requests){var j=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});j.add({title:"Sequencing Requests",content:"requests/index"});j.add({title:"Find Samples",content:"requests/find_samples_index"});j.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(j)}var c={id:"visualization",title:"Visualization",content:"visualization/list",title_attribute:"Visualize datasets"};if(!this.options.user.valid){c.disabled=true}var m=new b.GalaxyMastheadTab(c);if(this.options.user.valid){m.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});m.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"})}this.masthead.append(m);if(this.options.enable_cloud_launch){var f=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});f.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(f)}if(this.options.is_admin_user){var h=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only",title_attribute:"Administer this Galaxy"});this.masthead.append(h)}var l=new b.GalaxyMastheadTab({id:"help",title:"Help",title_attribute:"Support, contact, and community hubs"});if(this.options.biostar_url){l.add({title:"Galaxy Q&A Site",content:this.options.biostar_url,target:"_blank"});l.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}l.add({title:"Support",content:this.options.support_url,target:"_blank"});l.add({title:"Search",content:this.options.search_url,target:"_blank"});l.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});l.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});l.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});l.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(this.options.terms_url){l.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(l);if(!this.options.user.valid){var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only",title_attribute:"Account registration or login"});k.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){k.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(k)}else{var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only",title_attribute:"Account preferences and saved data"});k.add({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){k.add({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{k.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});k.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});k.add({title:"Logout",content:"user/logout",target:"_top",divider:true})}k.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});k.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});k.add({title:"Saved Pages",content:"page/list",target:"_top"});k.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){k.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(k)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file diff -r a0ccb7e6bfdfe5058561e709a81dee9f26e5c991 -r 5fd196b5d1760d1a8180184f8e5450e0957b37c2 templates/webapps/galaxy/dataset/errors.mako --- a/templates/webapps/galaxy/dataset/errors.mako +++ b/templates/webapps/galaxy/dataset/errors.mako @@ -103,7 +103,7 @@ </div><div class="form-row"><input type="submit" name="submit_error_report" value="Report" onclick="return sendReport( this, this.form, '_self' );"/> - %if trans.app.config.biostar_url: + %if trans.app.config.biostar_url and trans.app.config.biostar_enable_bug_reports: <input type="submit" name="submit_error_report" value="Post on Biostar" onclick="return sendReport( this, this.form, '_blank', true );"/> %endif </div> diff -r a0ccb7e6bfdfe5058561e709a81dee9f26e5c991 -r 5fd196b5d1760d1a8180184f8e5450e0957b37c2 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -41,7 +41,6 @@ 'enable_cloud_launch' : app.config.get_bool('enable_cloud_launch', False), 'lims_doc_url' : app.config.get("lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts"), 'biostar_url' : app.config.biostar_url, - 'biostar_url_redirect' : h.url_for( controller='biostar', action='biostar_redirect', biostar_action='show_tags', qualified=True ), 'support_url' : app.config.get("support_url", "http://wiki.galaxyproject.org/Support"), 'search_url' : app.config.get("search_url", "http://galaxyproject.org/search/usegalaxy/"), 'mailing_lists' : app.config.get("mailing_lists", "http://wiki.galaxyproject.org/MailingLists"), 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.