commit/galaxy-central: greg: More quickly stop the process of checking for migrated tools when starting Galaxy if there is no internet connection to the tool shed.
by commits-noreply＠bitbucket.org 22 Apr '14
by commits-noreply＠bitbucket.org 22 Apr '14
22 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e7ec387cb3b3/
Changeset: e7ec387cb3b3
User: greg
Date: 2014-04-22 17:45:10
Summary: More quickly stop the process of checking for migrated tools when starting Galaxy if there is no internet connection to the tool shed.
Affected #: 1 file
diff -r db35188ff312ac07b608bb51eef668fc8691dde8 -r e7ec387cb3b3b8e6aaceade0c8bdd3da0077ac57 lib/tool_shed/util/common_util.py
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -45,30 +45,37 @@
repository_name,
REPOSITORY_OWNER,
changeset_revision )
- # Accumulate all tool dependencies defined for repository dependencies for display to the user.
- for rd_key, rd_tups in repository_dependencies_dict.items():
- if rd_key in [ 'root_key', 'description' ]:
- continue
- for rd_tup in rd_tups:
- tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
- parse_repository_dependency_tuple( rd_tup )
+ if tool_shed_accessible:
+ # Accumulate all tool dependencies defined for repository dependencies for display to the user.
+ for rd_key, rd_tups in repository_dependencies_dict.items():
+ if rd_key in [ 'root_key', 'description' ]:
+ continue
+ for rd_tup in rd_tups:
+ tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
+ parse_repository_dependency_tuple( rd_tup )
+ tool_shed_accessible, tool_dependencies = get_tool_dependencies( app,
+ tool_shed_url,
+ name,
+ owner,
+ changeset_revision )
+ all_tool_dependencies = accumulate_tool_dependencies( tool_shed_accessible, tool_dependencies, all_tool_dependencies )
tool_shed_accessible, tool_dependencies = get_tool_dependencies( app,
tool_shed_url,
- name,
- owner,
+ repository_name,
+ REPOSITORY_OWNER,
changeset_revision )
all_tool_dependencies = accumulate_tool_dependencies( tool_shed_accessible, tool_dependencies, all_tool_dependencies )
- tool_shed_accessible, tool_dependencies = get_tool_dependencies( app, tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision )
- all_tool_dependencies = accumulate_tool_dependencies( tool_shed_accessible, tool_dependencies, all_tool_dependencies )
- for tool_elem in elem.findall( 'tool' ):
- tool_config_file_name = tool_elem.get( 'file' )
- if tool_config_file_name:
- # We currently do nothing with repository dependencies except install them (we do not display repositories that will be
- # installed to the user). However, we'll store them in the following dictionary in case we choose to display them in the
- # future.
- dependencies_dict = dict( tool_dependencies=all_tool_dependencies,
- repository_dependencies=repository_dependencies )
- migrated_tool_configs_dict[ tool_config_file_name ] = dependencies_dict
+ for tool_elem in elem.findall( 'tool' ):
+ tool_config_file_name = tool_elem.get( 'file' )
+ if tool_config_file_name:
+ # We currently do nothing with repository dependencies except install them (we do not display repositories that will be
+ # installed to the user). However, we'll store them in the following dictionary in case we choose to display them in the
+ # future.
+ dependencies_dict = dict( tool_dependencies=all_tool_dependencies,
+ repository_dependencies=repository_dependencies )
+ migrated_tool_configs_dict[ tool_config_file_name ] = dependencies_dict
+ else:
+ break
if tool_shed_accessible:
# Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names.
for tool_panel_config in tool_panel_configs:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: rename biostar menu link
by commits-noreply＠bitbucket.org 22 Apr '14
by commits-noreply＠bitbucket.org 22 Apr '14
22 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/db35188ff312/
Changeset: db35188ff312
User: martenson
Date: 2014-04-22 16:53:35
Summary: rename biostar menu link
Affected #: 2 files
diff -r aac938e8ba6f11adaa2240560a13cca7263025b0 -r db35188ff312ac07b608bb51eef668fc8691dde8 static/scripts/galaxy.menu.js
--- a/static/scripts/galaxy.menu.js
+++ b/static/scripts/galaxy.menu.js
@@ -195,7 +195,7 @@
if (this.options.biostar_url)
{
tab_help.add({
- title : "Galaxy Q&A Site",
+ title : "Galaxy Biostar",
content : this.options.biostar_url_redirect,
target : "_blank"
});
diff -r aac938e8ba6f11adaa2240560a13cca7263025b0 -r db35188ff312ac07b608bb51eef668fc8691dde8 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 Biostar",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
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Handle case where no network is available when attempting to determine repository dependencies for an installed repository.
by commits-noreply＠bitbucket.org 22 Apr '14
by commits-noreply＠bitbucket.org 22 Apr '14
22 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/aac938e8ba6f/
Changeset: aac938e8ba6f
User: greg
Date: 2014-04-22 16:33:42
Summary: Handle case where no network is available when attempting to determine repository dependencies for an installed repository.
Affected #: 1 file
diff -r 4f4725c1b0ef515a3b8d2e9b62322a6de3feaa32 -r aac938e8ba6f11adaa2240560a13cca7263025b0 lib/tool_shed/util/repository_dependency_util.py
--- a/lib/tool_shed/util/repository_dependency_util.py
+++ b/lib/tool_shed/util/repository_dependency_util.py
@@ -361,7 +361,11 @@
str( repository.changeset_revision ) )
url = common_util.url_join( tool_shed_url,
'repository/get_repository_dependencies%s' % params )
- raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
+ try:
+ raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
+ except Exception, e:
+ print "The URL\n%s\nraised the exception:\n%s\n" % ( url, str( e ) )
+ return ''
if len( raw_text ) > 2:
encoded_text = json.from_json_string( raw_text )
text = encoding_util.tool_shed_decode( encoded_text )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: davebgx: Merge stable changes into default.
by commits-noreply＠bitbucket.org 22 Apr '14
by commits-noreply＠bitbucket.org 22 Apr '14
22 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4f4725c1b0ef/
Changeset: 4f4725c1b0ef
User: davebgx
Date: 2014-04-22 16:09:40
Summary: Merge stable changes into default.
Affected #: 1 file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Merged in dan/galaxy-central-stable-prs/stable (pull request #374)
by commits-noreply＠bitbucket.org 22 Apr '14
by commits-noreply＠bitbucket.org 22 Apr '14
22 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1d06e19aa3aa/
Changeset: 1d06e19aa3aa
Branch: stable
User: dannon
Date: 2014-04-22 16:01:58
Summary: Merged in dan/galaxy-central-stable-prs/stable (pull request #374)
Prevent redirect misuse on user log in.
Affected #: 2 files
diff -r 7fe7330660189bb382191a18ee145a7698ddbb74 -r 1d06e19aa3aac0c87b21f8482b8fc73c89e277ad lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -29,6 +29,8 @@
from hashlib import md5
from itertools import izip
+from urlparse import urlparse
+
from galaxy import eggs
eggs.require( 'docutils' )
@@ -691,6 +693,17 @@
def string_to_object( s ):
return pickle.loads( binascii.unhexlify( s ) )
+def compare_urls( url1, url2, compare_scheme=True, compare_hostname=True, compare_path=True ):
+ url1 = urlparse( url1 )
+ url2 = urlparse( url2 )
+ if compare_scheme and url1.scheme and url2.scheme and url1.scheme != url2.scheme:
+ return False
+ if compare_hostname and url1.hostname and url2.hostname and url1.hostname != url2.hostname:
+ return False
+ if compare_path and url1.path and url2.path and url1.path != url2.path:
+ return False
+ return True
+
def get_ucsc_by_build(build):
sites = []
for site in ucsc_build_sites:
diff -r 7fe7330660189bb382191a18ee145a7698ddbb74 -r 1d06e19aa3aac0c87b21f8482b8fc73c89e277ad lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -445,26 +445,35 @@
return self.user_openid_grid( trans, **kwd )
@web.expose
- def login( self, trans, redirect_url='', refresh_frames=[], **kwd ):
+ def login( self, trans, refresh_frames=[], **kwd ):
'''Handle Galaxy Log in'''
redirect = kwd.get( 'redirect', trans.request.referer ).strip()
+ root_url = url_for( '/', qualified=True )
+ redirect_url = '' #always start with redirect_url being empty
+ # compare urls, to prevent a redirect from pointing (directly) outside of galaxy
+ # or to enter a logout/login loop
+ if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ):
+ redirect = root_url
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
header = ''
- user = None
+ user = trans.user
email = kwd.get( 'email', '' )
- if kwd.get( 'login_button', False ):
+ if user:
+ #already logged in
+ redirect_url = redirect
+ message = 'You are already logged in.'
+ status = 'info'
+ elif kwd.get( 'login_button', False ):
if trans.webapp.name == 'galaxy' and not refresh_frames:
if trans.app.config.require_login:
refresh_frames = [ 'masthead', 'history', 'tools' ]
else:
refresh_frames = [ 'masthead', 'history' ]
message, status, user, success = self.__validate_login( trans, **kwd )
- if success and redirect and not redirect.startswith( trans.request.base + url_for( controller='user', action='logout' ) ):
+ if success:
redirect_url = redirect
- elif success:
- redirect_url = url_for( '/' )
if not user and trans.app.config.require_login:
if trans.app.config.allow_user_creation:
create_account_str = " If you don't already have an account, <a href='%s'>you may create one</a>." % \
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3e87c1b1c380/
Changeset: 3e87c1b1c380
Branch: stable
User: dan
Date: 2014-04-21 18:11:49
Summary: Prevent redirect misuse on user log in.
Affected #: 2 files
diff -r e6876f6918548a0805fa0cc5306ba1ced6fb184a -r 3e87c1b1c3801aac29bb9bd7709ead6f996d7dc3 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -29,6 +29,8 @@
from hashlib import md5
from itertools import izip
+from urlparse import urlparse
+
from galaxy import eggs
eggs.require( 'docutils' )
@@ -691,6 +693,17 @@
def string_to_object( s ):
return pickle.loads( binascii.unhexlify( s ) )
+def compare_urls( url1, url2, compare_scheme=True, compare_hostname=True, compare_path=True ):
+ url1 = urlparse( url1 )
+ url2 = urlparse( url2 )
+ if compare_scheme and url1.scheme and url2.scheme and url1.scheme != url2.scheme:
+ return False
+ if compare_hostname and url1.hostname and url2.hostname and url1.hostname != url2.hostname:
+ return False
+ if compare_path and url1.path and url2.path and url1.path != url2.path:
+ return False
+ return True
+
def get_ucsc_by_build(build):
sites = []
for site in ucsc_build_sites:
diff -r e6876f6918548a0805fa0cc5306ba1ced6fb184a -r 3e87c1b1c3801aac29bb9bd7709ead6f996d7dc3 lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -445,26 +445,35 @@
return self.user_openid_grid( trans, **kwd )
@web.expose
- def login( self, trans, redirect_url='', refresh_frames=[], **kwd ):
+ def login( self, trans, refresh_frames=[], **kwd ):
'''Handle Galaxy Log in'''
redirect = kwd.get( 'redirect', trans.request.referer ).strip()
+ root_url = url_for( '/', qualified=True )
+ redirect_url = '' #always start with redirect_url being empty
+ # compare urls, to prevent a redirect from pointing (directly) outside of galaxy
+ # or to enter a logout/login loop
+ if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ):
+ redirect = root_url
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
header = ''
- user = None
+ user = trans.user
email = kwd.get( 'email', '' )
- if kwd.get( 'login_button', False ):
+ if user:
+ #already logged in
+ redirect_url = redirect
+ message = 'You are already logged in.'
+ status = 'info'
+ elif kwd.get( 'login_button', False ):
if trans.webapp.name == 'galaxy' and not refresh_frames:
if trans.app.config.require_login:
refresh_frames = [ 'masthead', 'history', 'tools' ]
else:
refresh_frames = [ 'masthead', 'history' ]
message, status, user, success = self.__validate_login( trans, **kwd )
- if success and redirect and not redirect.startswith( trans.request.base + url_for( controller='user', action='logout' ) ):
+ if success:
redirect_url = redirect
- elif success:
- redirect_url = url_for( '/' )
if not user and trans.app.config.require_login:
if trans.app.config.allow_user_creation:
create_account_str = " If you don't already have an account, <a href='%s'>you may create one</a>." % \
https://bitbucket.org/galaxy/galaxy-central/commits/6e91e5fcd113/
Changeset: 6e91e5fcd113
Branch: stable
User: dan
Date: 2014-04-21 18:12:03
Summary: Fix for masthead link for biostar mainpage.
Affected #: 3 files
diff -r 3e87c1b1c3801aac29bb9bd7709ead6f996d7dc3 -r 6e91e5fcd11351ea04789403e44002f9ccb70060 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,
+ content : this.options.biostar_url_redirect,
target : "_blank"
});
tab_help.add({
diff -r 3e87c1b1c3801aac29bb9bd7709ead6f996d7dc3 -r 6e91e5fcd11351ea04789403e44002f9ccb70060 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,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_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
diff -r 3e87c1b1c3801aac29bb9bd7709ead6f996d7dc3 -r 6e91e5fcd11351ea04789403e44002f9ccb70060 templates/webapps/galaxy/galaxy.masthead.mako
--- a/templates/webapps/galaxy/galaxy.masthead.mako
+++ b/templates/webapps/galaxy/galaxy.masthead.mako
@@ -41,6 +41,7 @@
'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', 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"),
https://bitbucket.org/galaxy/galaxy-central/commits/1d06e19aa3aa/
Changeset: 1d06e19aa3aa
Branch: stable
User: dannon
Date: 2014-04-22 16:01:58
Summary: Merged in dan/galaxy-central-stable-prs/stable (pull request #374)
Prevent redirect misuse on user log in.
Affected #: 2 files
diff -r 7fe7330660189bb382191a18ee145a7698ddbb74 -r 1d06e19aa3aac0c87b21f8482b8fc73c89e277ad lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -29,6 +29,8 @@
from hashlib import md5
from itertools import izip
+from urlparse import urlparse
+
from galaxy import eggs
eggs.require( 'docutils' )
@@ -691,6 +693,17 @@
def string_to_object( s ):
return pickle.loads( binascii.unhexlify( s ) )
+def compare_urls( url1, url2, compare_scheme=True, compare_hostname=True, compare_path=True ):
+ url1 = urlparse( url1 )
+ url2 = urlparse( url2 )
+ if compare_scheme and url1.scheme and url2.scheme and url1.scheme != url2.scheme:
+ return False
+ if compare_hostname and url1.hostname and url2.hostname and url1.hostname != url2.hostname:
+ return False
+ if compare_path and url1.path and url2.path and url1.path != url2.path:
+ return False
+ return True
+
def get_ucsc_by_build(build):
sites = []
for site in ucsc_build_sites:
diff -r 7fe7330660189bb382191a18ee145a7698ddbb74 -r 1d06e19aa3aac0c87b21f8482b8fc73c89e277ad lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -445,26 +445,35 @@
return self.user_openid_grid( trans, **kwd )
@web.expose
- def login( self, trans, redirect_url='', refresh_frames=[], **kwd ):
+ def login( self, trans, refresh_frames=[], **kwd ):
'''Handle Galaxy Log in'''
redirect = kwd.get( 'redirect', trans.request.referer ).strip()
+ root_url = url_for( '/', qualified=True )
+ redirect_url = '' #always start with redirect_url being empty
+ # compare urls, to prevent a redirect from pointing (directly) outside of galaxy
+ # or to enter a logout/login loop
+ if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ):
+ redirect = root_url
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
header = ''
- user = None
+ user = trans.user
email = kwd.get( 'email', '' )
- if kwd.get( 'login_button', False ):
+ if user:
+ #already logged in
+ redirect_url = redirect
+ message = 'You are already logged in.'
+ status = 'info'
+ elif kwd.get( 'login_button', False ):
if trans.webapp.name == 'galaxy' and not refresh_frames:
if trans.app.config.require_login:
refresh_frames = [ 'masthead', 'history', 'tools' ]
else:
refresh_frames = [ 'masthead', 'history' ]
message, status, user, success = self.__validate_login( trans, **kwd )
- if success and redirect and not redirect.startswith( trans.request.base + url_for( controller='user', action='logout' ) ):
+ if success:
redirect_url = redirect
- elif success:
- redirect_url = url_for( '/' )
if not user and trans.app.config.require_login:
if trans.app.config.allow_user_creation:
create_account_str = " If you don't already have an account, <a href='%s'>you may create one</a>." % \
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Fix for masthead link for biostar mainpage.
by commits-noreply＠bitbucket.org 22 Apr '14
by commits-noreply＠bitbucket.org 22 Apr '14
22 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7fe733066018/
Changeset: 7fe733066018
Branch: stable
User: dan
Date: 2014-04-21 18:12:03
Summary: Fix for masthead link for biostar mainpage.
Affected #: 3 files
diff -r e6876f6918548a0805fa0cc5306ba1ced6fb184a -r 7fe7330660189bb382191a18ee145a7698ddbb74 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,
+ content : this.options.biostar_url_redirect,
target : "_blank"
});
tab_help.add({
diff -r e6876f6918548a0805fa0cc5306ba1ced6fb184a -r 7fe7330660189bb382191a18ee145a7698ddbb74 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,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_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
diff -r e6876f6918548a0805fa0cc5306ba1ced6fb184a -r 7fe7330660189bb382191a18ee145a7698ddbb74 templates/webapps/galaxy/galaxy.masthead.mako
--- a/templates/webapps/galaxy/galaxy.masthead.mako
+++ b/templates/webapps/galaxy/galaxy.masthead.mako
@@ -41,6 +41,7 @@
'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', 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/
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commit/galaxy-central: martenson: data libraries: improved chaincall for importing datasets into history, some cleanup
by commits-noreply＠bitbucket.org 21 Apr '14
by commits-noreply＠bitbucket.org 21 Apr '14
21 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c5cea7463833/
Changeset: c5cea7463833
User: martenson
Date: 2014-04-21 23:31:36
Summary: data libraries: improved chaincall for importing datasets into history, some cleanup
Affected #: 4 files
diff -r 557c0f2c6129026d8a6738292a4ae26e681e1391 -r c5cea74638335a586c2d498ccb13dd5d23085b31 static/scripts/galaxy.library.js
--- a/static/scripts/galaxy.library.js
+++ b/static/scripts/galaxy.library.js
@@ -2,7 +2,6 @@
// === MAIN GALAXY LIBRARY MODULE ====
// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
-// dependencies
define([
"galaxy.masthead",
"utils/utils",
@@ -26,7 +25,7 @@
) {
// ============================================================================
-//ROUTER
+// ROUTER
var LibraryRouter = Backbone.Router.extend({
routes: {
"" : "libraries",
@@ -48,11 +47,13 @@
// ============================================================================
// Main controller of Galaxy Library
var GalaxyLibrary = Backbone.View.extend({
+
libraryToolbarView: null,
libraryListView: null,
library_router: null,
folderToolbarView: null,
folderListView: null,
+
initialize : function(){
Galaxy.libraries = this;
@@ -79,11 +80,7 @@
this.library_router.on('route:download', function(folder_id, format) {
if ($('#center').find(':checked').length === 0) {
mod_toastr.info('You have to select some datasets to download')
- // this happens rarely when there is a server/data error and client gets an actual response instead of an attachment
- // we don't know what was selected so we can't download again, we redirect to the folder provided
- Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true});
} else {
- // send download stream
Galaxy.libraries.folderToolbarView.download(folder_id, format);
Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true});
}
diff -r 557c0f2c6129026d8a6738292a4ae26e681e1391 -r c5cea74638335a586c2d498ccb13dd5d23085b31 static/scripts/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/mvc/library/library-foldertoolbar-view.js
@@ -20,7 +20,7 @@
defaults: {
'can_add_library_item' : false,
'contains_file' : false,
- 'adding_datasets' : {
+ 'chain_call_control' : {
'total_number' : 0,
'failed_number' : 0
}
@@ -153,7 +153,12 @@
success: function (){
callback(self);
},
- error: function(){
+ error: function(model, response){
+ if (typeof response.responseJSON !== "undefined"){
+ mod_toastr.error(response.responseJSON.err_msg);
+ } else {
+ mod_toastr.error('An error ocurred :(');
+ }
}
});
},
@@ -163,6 +168,10 @@
// disable the button to prevent multiple submission
this.modal.disableButton('Import');
+ // init the control counters
+ this.options.chain_call_control.total_number = 0;
+ this.options.chain_call_control.failed_number = 0;
+
var history_id = $("select[name=dataset_import_bulk] option:selected").val();
// we can save last used history to pre-select it next time
this.options.last_used_history_id = history_id;
@@ -191,6 +200,7 @@
historyItem.source = 'library';
datasets_to_import.push(historyItem);
}
+ this.options.chain_call_control.total_number = datasets_to_import.length;
// call the recursive function to call ajax one after each other (request FIFO queue)
this.chainCall(datasets_to_import, history_name);
},
@@ -199,18 +209,26 @@
var self = this;
var popped_item = history_item_set.pop();
if (typeof popped_item === "undefined") {
- mod_toastr.success('Datasets were imported to history: ' + history_name);
- this.modal.hide();
- return;
+ if (this.options.chain_call_control.failed_number === 0){
+ mod_toastr.success('Selected datasets imported into history');
+ } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number){
+ mod_toastr.error('There was an error and no datasets were imported into history.');
+ } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number){
+ mod_toastr.warning('Some of the datasets could not be imported into history');
+ }
+ Galaxy.modal.hide();
+ return;
}
var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source}));
promise.done(function(a1){
+ // we are fine
self.updateProgress();
self.chainCall(history_item_set, history_name);
})
.fail(function(a1){
- mod_toastr.error('An error occured :(');
+ // we have a problem
+ self.options.chain_call_control.failed_number += 1;
self.updateProgress();
self.chainCall(history_item_set, history_name);
});
@@ -307,9 +325,9 @@
addAllDatasetsFromHistory : function (){
// disable the button to prevent multiple submission
this.modal.disableButton('Add');
- // init the counters
- this.options.adding_datasets.total_number = 0;
- this.options.adding_datasets.failed_number = 0;
+ // init the control counters
+ this.options.chain_call_control.total_number = 0;
+ this.options.chain_call_control.failed_number = 0;
var history_dataset_ids = [];
this.modal.$el.find('#selected_history_content').find(':checked').each(function(){
@@ -335,7 +353,7 @@
folder_item.set({'from_hda_id':history_dataset_id});
hdas_to_add.push(folder_item);
}
- this.options.adding_datasets.total_number = hdas_to_add.length;
+ this.options.chain_call_control.total_number = hdas_to_add.length;
// call the recursive function to call ajax one after each other (request FIFO queue)
this.chainCallAddingHdas(hdas_to_add);
},
@@ -345,11 +363,11 @@
this.added_hdas = new mod_library_model.Folder();
var popped_item = hdas_set.pop();
if (typeof popped_item === "undefined") {
- if (this.options.adding_datasets.failed_number === 0){
+ if (this.options.chain_call_control.failed_number === 0){
mod_toastr.success('Selected datasets from history added to the folder');
- } else if (this.options.adding_datasets.failed_number === this.options.adding_datasets.total_number){
+ } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number){
mod_toastr.error('There was an error and no datasets were added to the folder.');
- } else if (this.options.adding_datasets.failed_number < this.options.adding_datasets.total_number){
+ } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number){
mod_toastr.warning('Some of the datasets could not be added to the folder');
}
Galaxy.modal.hide();
@@ -365,12 +383,7 @@
})
.fail(function(data){
// we have a problem
- self.options.adding_datasets.failed_number += 1;
- // if (typeof data.responseJSON !== "undefined"){
- // mod_toastr.error(data.responseJSON.err_msg);
- // } else {
- // mod_toastr.error('An error ocurred :(');
- // }
+ self.options.chain_call_control.failed_number += 1;
self.updateProgress();
self.chainCallAddingHdas(hdas_set);
});
diff -r 557c0f2c6129026d8a6738292a4ae26e681e1391 -r c5cea74638335a586c2d498ccb13dd5d23085b31 static/scripts/packed/galaxy.library.js
--- a/static/scripts/packed/galaxy.library.js
+++ b/static/scripts/packed/galaxy.library.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#center").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#center").find(":checked").length===0){g.info("You have to select some datasets to download")}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}});
\ No newline at end of file
diff -r 557c0f2c6129026d8a6738292a4ae26e681e1391 -r c5cea74638335a586c2d498ccb13dd5d23085b31 static/scripts/packed/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal"},defaults:{can_add_library_item:false,contains_file:false,adding_datasets:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g=false;if(Galaxy.currUser){g=Galaxy.currUser.isAdmin()}this.$el.html(h({id:this.options.id,admin_user:g}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$("#toolbtn_create_folder").show();$(".toolbtn_add_files").show()}if(this.options.contains_file===true){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(){}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var j=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=j;var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(n({history_name:m}));var k=100/o.length;this.initProgress(k);var f=[];for(var g=o.length-1;g>=0;g--){var h=o[g];var l=new c.HistoryItem();l.url=l.urlRoot+j+"/contents";l.content=h;l.source="library";f.push(l)}this.chainCall(f,m)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){e.success("Datasets were imported to history: "+j);this.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(k){f.updateProgress();f.chainCall(g,j)}).fail(function(k){e.error("An error occured :(");f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(j,i){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.adding_datasets.total_number=0;this.options.adding_datasets.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.adding_datasets.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.adding_datasets.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.adding_datasets.failed_number===this.options.adding_datasets.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.adding_datasets.failed_number<this.options.adding_datasets.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(j){f.options.adding_datasets.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<div id="library_folder_toolbar" >');tmpl_array.push('<div class="btn-group">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("</div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; " type="button"><span class="fa fa-book"></span> to history</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; ">');tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g=false;if(Galaxy.currUser){g=Galaxy.currUser.isAdmin()}this.$el.html(h({id:this.options.id,admin_user:g}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$("#toolbtn_create_folder").show();$(".toolbtn_add_files").show()}if(this.options.contains_file===true){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var j=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=j;var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(n({history_name:m}));var k=100/o.length;this.initProgress(k);var f=[];for(var g=o.length-1;g>=0;g--){var h=o[g];var l=new c.HistoryItem();l.url=l.urlRoot+j+"/contents";l.content=h;l.source="library";f.push(l)}this.options.chain_call_control.total_number=f.length;this.chainCall(f,m)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history")}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(k){f.updateProgress();f.chainCall(g,j)}).fail(function(k){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(j,i){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(j){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<div id="library_folder_toolbar" >');tmpl_array.push('<div class="btn-group">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("</div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; " type="button"><span class="fa fa-book"></span> to history</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; ">');tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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5 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e51282a5b1bf/
Changeset: e51282a5b1bf
User: dannon
Date: 2014-02-22 15:25:20
Summary: Cloudlaunch cleanup/pep8
Affected #: 1 file
diff -r fac578cca75887d811e67993a655fed20c0d8713 -r e51282a5b1bff80518db274800c2be7de2968785 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -11,13 +11,14 @@
import os
import tempfile
import time
-import pkg_resources
+
from galaxy import eggs
-pkg_resources.require('boto')
-import boto
from galaxy import web
from galaxy.web.base.controller import BaseUIController
from galaxy.util.json import to_json_string
+
+eggs.require('boto')
+import boto
from boto.ec2.regioninfo import RegionInfo
from boto.exception import EC2ResponseError, S3ResponseError
from boto.s3.connection import OrdinaryCallingFormat, S3Connection
@@ -29,20 +30,24 @@
class CloudController(BaseUIController):
+ """Galaxy Cloud Functions"""
def __init__(self, app):
BaseUIController.__init__(self, app)
@web.expose
- def index(self, trans, share_string=None, ami=None, bucket_default = None):
+ def index(self, trans, share_string=None, ami=None, bucket_default=None):
+ """
+ Serves the default page requesting AWS keys
+ """
return trans.fill_template("cloud/index.mako",
- default_keypair = DEFAULT_KEYPAIR,
- share_string=share_string,
- ami=ami,
- bucket_default=bucket_default)
+ default_keypair=DEFAULT_KEYPAIR,
+ share_string=share_string,
+ ami=ami,
+ bucket_default=bucket_default)
@web.expose
- def get_account_info(self, trans, key_id, secret, **kwargs):
+ def get_account_info(self, trans, key_id, secret):
"""
Get EC2 Account Info
"""
@@ -54,7 +59,7 @@
except EC2ResponseError, e:
log.error("Problem starting an instance: %s\n%s" % (e, e.body))
trans.response.status = 400
- return e.error_message or "Instance failure, but no specific error was detected. Please check your AWS Console."
+ return e.error_message or "Error retrieving account information. Please verify your credentials are correct, and contact galaxy support to report this issue."
account_info['keypairs'] = [akp.name for akp in kps]
#Existing Clusters
s3_conn = S3Connection(key_id, secret, calling_format=OrdinaryCallingFormat())
@@ -79,7 +84,7 @@
for line in pd_contents.split('\n'):
if 'vol_id' in line:
vol_id = line.split(':')[1].strip()
- v = ec2_conn.get_all_volumes(volume_ids = [vol_id])
+ v = ec2_conn.get_all_volumes(volume_ids=[vol_id])
if v:
zone = v[0].zone
else:
@@ -91,7 +96,7 @@
if key.name.endswith('.clusterName'):
clusters.append({'name': key.name.split('.clusterName')[0],
'persistent_data': pd_contents,
- 'zone':zone})
+ 'zone': zone})
account_info['clusters'] = clusters
account_info['zones'] = [z.name for z in ec2_conn.get_all_zones()]
return to_json_string(account_info)
@@ -111,29 +116,25 @@
return ec2_error
else:
user_provided_data = {'cluster_name': cluster_name,
- 'access_key': key_id,
- 'secret_key': secret,
- 'instance_type': instance_type}
+ 'access_key': key_id,
+ 'secret_key': secret,
+ 'instance_type': instance_type}
if password:
user_provided_data['password'] = password
if share_string:
user_provided_data['share_string'] = share_string
if bucket_default:
- user_provided_data['bucket_default'] = bucket_default
-
+ user_provided_data['bucket_default'] = bucket_default
if not ami:
ami = trans.app.config.cloudlaunch_default_ami
-
rs = run_instance(ec2_conn=ec2_conn,
- image_id = ami,
- user_provided_data=user_provided_data,
- key_name=kp_name,
- security_groups=[sg_name],
- placement=zone
- )
+ image_id=ami,
+ user_provided_data=user_provided_data,
+ key_name=kp_name,
+ security_groups=[sg_name],
+ placement=zone)
if rs:
instance = rs.instances[0]
- ct = 0
while not instance.public_dns_name:
try:
instance.update()
@@ -141,7 +142,6 @@
#This can happen when update is invoked before the instance is fully registered.
#Prevent failure, wait it out.
pass
- ct += 1
time.sleep(1)
if kp_material:
#We have created a keypair. Save to tempfile for one time retrieval.
@@ -152,14 +152,12 @@
kp_material_tag = fname[fname.rfind(PKEY_PREFIX) + len(PKEY_PREFIX):]
else:
kp_material_tag = None
- return to_json_string({
- 'cluster_name': cluster_name,
- 'instance_id': rs.instances[0].id,
- 'image_id': rs.instances[0].image_id,
- 'public_dns_name': rs.instances[0].public_dns_name,
- 'kp_name': kp_name,
- 'kp_material_tag':kp_material_tag
- })
+ return to_json_string({'cluster_name': cluster_name,
+ 'instance_id': rs.instances[0].id,
+ 'image_id': rs.instances[0].image_id,
+ 'public_dns_name': rs.instances[0].public_dns_name,
+ 'kp_name': kp_name,
+ 'kp_material_tag': kp_material_tag})
else:
trans.response.status = 400
return "Instance failure, but no specific error was detected. Please check your AWS Console."
@@ -173,16 +171,17 @@
kp_material = f.read()
f.close()
trans.response.headers['Content-Length'] = int( os.stat( expected_path ).st_size )
- trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename
+ trans.response.set_content_type( "application/octet-stream" ) # force octet-stream so Safari doesn't append mime extensions to filename
trans.response.headers["Content-Disposition"] = 'attachment; filename="%s.pem"' % DEFAULT_KEYPAIR
os.remove(expected_path)
return kp_material
trans.response.status = 400
return "Invalid identifier"
-# ## Cloud interaction methods
+
def connect_ec2(a_key, s_key):
- """ Create and return an EC2 connection object.
+ """
+ Create and return an EC2 connection object.
"""
# Use variables for forward looking flexibility
# AWS connection values
@@ -193,14 +192,15 @@
ec2_conn_path = '/'
r = RegionInfo(name=region_name, endpoint=region_endpoint)
ec2_conn = boto.connect_ec2(aws_access_key_id=a_key,
- aws_secret_access_key=s_key,
- api_version='2011-11-01', # needed for availability zone support
- is_secure=is_secure,
- region=r,
- port=ec2_port,
- path=ec2_conn_path)
+ aws_secret_access_key=s_key,
+ api_version='2011-11-01', # needed for availability zone support
+ is_secure=is_secure,
+ region=r,
+ port=ec2_port,
+ path=ec2_conn_path)
return ec2_conn
+
def create_cm_security_group(ec2_conn, sg_name='CloudMan'):
""" Create a security group with all authorizations required to run CloudMan.
If the group already exists, check its rules and add the missing ones.
@@ -220,11 +220,11 @@
cmsg = ec2_conn.create_security_group(sg_name, 'A security group for CloudMan')
# Add appropriate authorization rules
# If these rules already exist, nothing will be changed in the SG
- ports = (('80', '80'), # Web UI
- ('20', '21'), # FTP
- ('22', '22'), # ssh
- ('30000', '30100'), # FTP transfer
- ('42284', '42284')) # CloudMan UI
+ ports = (('80', '80'), # Web UI
+ ('20', '21'), # FTP
+ ('22', '22'), # ssh
+ ('30000', '30100'), # FTP transfer
+ ('42284', '42284')) # CloudMan UI
for port in ports:
try:
if not rule_exists(cmsg.rules, from_port=port[0], to_port=port[1]):
@@ -234,7 +234,7 @@
except EC2ResponseError, e:
log.error("A problem with security group authorizations: %s" % e)
# Add rule that allows communication between instances in the same SG
- g_rule_exists = False # Flag to indicate if group rule already exists
+ g_rule_exists = False # Flag to indicate if group rule already exists
for rule in cmsg.rules:
for grant in rule.grants:
if grant.name == cmsg.name:
@@ -250,6 +250,7 @@
log.info("Done configuring '%s' security group" % cmsg.name)
return cmsg.name
+
def rule_exists(rules, from_port, to_port, ip_protocol='tcp', cidr_ip='0.0.0.0/0'):
""" A convenience method to check if an authorization rule in a security
group exists.
@@ -260,6 +261,7 @@
return True
return False
+
def create_key_pair(ec2_conn, key_name=DEFAULT_KEYPAIR):
""" Create a key pair with the provided name.
Return the name of the key or None if there was an error creating the key.
@@ -279,6 +281,7 @@
return None, None
return kp.name, kp.material
+
def run_instance(ec2_conn, user_provided_data, image_id=None,
kernel_id=None, ramdisk_id=None, key_name=DEFAULT_KEYPAIR,
placement=None, security_groups=['CloudMan']):
@@ -310,6 +313,7 @@
log.warning("Problem starting an instance?")
return rs
+
def _find_placement(ec2_conn, instance_type):
"""Find a region zone that supports our requested instance type.
@@ -328,4 +332,3 @@
return cur_loc
log.error("Did not find availabilty zone in {0} for {1}".format(base, instance_type))
return None
-
https://bitbucket.org/galaxy/galaxy-central/commits/e45c2616e207/
Changeset: e45c2616e207
User: dannon
Date: 2014-04-03 21:23:52
Summary: Incremental work / shifting changes to bioblend but committed here for posterity.
Affected #: 1 file
diff -r e51282a5b1bff80518db274800c2be7de2968785 -r e45c2616e207e25e4978d14343bd5bff495a16b0 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -3,10 +3,8 @@
Adapted from Brad Chapman and Enis Afgan's BioCloudCentral
BioCloudCentral Source: https://github.com/chapmanb/biocloudcentral
-
"""
-import datetime
import logging
import os
import tempfile
@@ -19,14 +17,19 @@
eggs.require('boto')
import boto
+import boto.vpc
from boto.ec2.regioninfo import RegionInfo
from boto.exception import EC2ResponseError, S3ResponseError
from boto.s3.connection import OrdinaryCallingFormat, S3Connection
log = logging.getLogger(__name__)
+logging.getLogger('boto').setLevel(logging.INFO)
+
+
PKEY_PREFIX = 'gxy_pkey'
DEFAULT_KEYPAIR = 'cloudman_keypair'
+CLOUDMAN_TAG_KEY = 'galaxy:cloudman'
class CloudController(BaseUIController):
@@ -51,7 +54,6 @@
"""
Get EC2 Account Info
"""
- #Keypairs
account_info = {}
try:
ec2_conn = connect_ec2(key_id, secret)
@@ -79,19 +81,7 @@
# This will also allow for much more sophisticated rendering of existing clusters
# Currently, this zone detection is a hack.
pd_contents = pd.get_contents_as_string()
- zone = ''
- try:
- for line in pd_contents.split('\n'):
- if 'vol_id' in line:
- vol_id = line.split(':')[1].strip()
- v = ec2_conn.get_all_volumes(volume_ids=[vol_id])
- if v:
- zone = v[0].zone
- else:
- zone = ''
- except:
- #If anything goes wrong with zone detection, use the default selection.
- zone = ''
+ zone = get_zone_from_pd(pd_contents, ec2_conn)
for key in bucket.list():
if key.name.endswith('.clusterName'):
clusters.append({'name': key.name.split('.clusterName')[0],
@@ -107,60 +97,51 @@
try:
# Create security group & key pair used when starting an instance
ec2_conn = connect_ec2(key_id, secret)
- sg_name = create_cm_security_group(ec2_conn)
+ sg = get_or_create_cm_security_group(ec2_conn)
kp_name, kp_material = create_key_pair(ec2_conn, key_name=keypair)
except EC2ResponseError, err:
ec2_error = err.error_message
if ec2_error:
trans.response.status = 400
return ec2_error
+ #Get an elastic ip, add to UserData.
+ user_provided_data = _format_user_data(cluster_name, key_id, secret, password, share_string, bucket_default)
+ if not ami:
+ ami = trans.app.config.cloudlaunch_default_ami
+ rs = _run_instance(ec2_conn=ec2_conn,
+ image_id=ami,
+ user_provided_data=user_provided_data,
+ key_name=kp_name,
+ security_group_ids=[sg.id],
+ placement=zone,
+ instance_type=instance_type,
+ subnet_id=get_or_create_cm_subnet(key_id, secret, zone).id)
+ if not rs:
+ trans.response.status = 400
+ return "Instance failure, but no specific error was detected. Please check your AWS Console."
+ instance = rs.instances[0]
+ while not instance.public_dns_name:
+ try:
+ instance.update()
+ except EC2ResponseError:
+ # This can happen when update is invoked before the instance is fully registered.
+ pass
+ time.sleep(1)
+ if kp_material:
+ #We have created a keypair. Save to tempfile for one time retrieval.
+ (fd, fname) = tempfile.mkstemp(prefix=PKEY_PREFIX, dir=trans.app.config.new_file_path)
+ f = os.fdopen(fd, 'wt')
+ f.write(kp_material)
+ f.close()
+ kp_material_tag = fname[fname.rfind(PKEY_PREFIX) + len(PKEY_PREFIX):]
else:
- user_provided_data = {'cluster_name': cluster_name,
- 'access_key': key_id,
- 'secret_key': secret,
- 'instance_type': instance_type}
- if password:
- user_provided_data['password'] = password
- if share_string:
- user_provided_data['share_string'] = share_string
- if bucket_default:
- user_provided_data['bucket_default'] = bucket_default
- if not ami:
- ami = trans.app.config.cloudlaunch_default_ami
- rs = run_instance(ec2_conn=ec2_conn,
- image_id=ami,
- user_provided_data=user_provided_data,
- key_name=kp_name,
- security_groups=[sg_name],
- placement=zone)
- if rs:
- instance = rs.instances[0]
- while not instance.public_dns_name:
- try:
- instance.update()
- except EC2ResponseError:
- #This can happen when update is invoked before the instance is fully registered.
- #Prevent failure, wait it out.
- pass
- time.sleep(1)
- if kp_material:
- #We have created a keypair. Save to tempfile for one time retrieval.
- (fd, fname) = tempfile.mkstemp(prefix=PKEY_PREFIX, dir=trans.app.config.new_file_path)
- f = os.fdopen(fd, 'wt')
- f.write(kp_material)
- f.close()
- kp_material_tag = fname[fname.rfind(PKEY_PREFIX) + len(PKEY_PREFIX):]
- else:
- kp_material_tag = None
- return to_json_string({'cluster_name': cluster_name,
- 'instance_id': rs.instances[0].id,
- 'image_id': rs.instances[0].image_id,
- 'public_dns_name': rs.instances[0].public_dns_name,
- 'kp_name': kp_name,
- 'kp_material_tag': kp_material_tag})
- else:
- trans.response.status = 400
- return "Instance failure, but no specific error was detected. Please check your AWS Console."
+ kp_material_tag = None
+ return to_json_string({'cluster_name': cluster_name,
+ 'instance_id': rs.instances[0].id,
+ 'image_id': rs.instances[0].image_id,
+ 'public_dns_name': rs.instances[0].public_dns_name,
+ 'kp_name': kp_name,
+ 'kp_material_tag': kp_material_tag})
@web.expose
def get_pkey(self, trans, kp_material_tag=None):
@@ -179,6 +160,21 @@
return "Invalid identifier"
+def get_zone_from_pd(pd_contents, ec2_conn):
+ try:
+ for line in pd_contents.split('\n'):
+ if 'vol_id' in line:
+ vol_id = line.split(':')[1].strip()
+ v = ec2_conn.get_all_volumes(volume_ids=[vol_id])
+ if v:
+ return v[0].zone
+ except:
+ # Things can go wrong with Zone detection outside of our control. Use
+ # the default zone if this happens.
+ pass
+ return ''
+
+
def connect_ec2(a_key, s_key):
"""
Create and return an EC2 connection object.
@@ -193,7 +189,6 @@
r = RegionInfo(name=region_name, endpoint=region_endpoint)
ec2_conn = boto.connect_ec2(aws_access_key_id=a_key,
aws_secret_access_key=s_key,
- api_version='2011-11-01', # needed for availability zone support
is_secure=is_secure,
region=r,
port=ec2_port,
@@ -201,23 +196,22 @@
return ec2_conn
-def create_cm_security_group(ec2_conn, sg_name='CloudMan'):
- """ Create a security group with all authorizations required to run CloudMan.
- If the group already exists, check its rules and add the missing ones.
- Return the name of the created security group.
+def get_or_create_cm_security_group(ec2_conn, sg_name='CloudManVPC'):
"""
- cmsg = None
- # Check if this security group already exists
- sgs = ec2_conn.get_all_security_groups()
- for sg in sgs:
- if sg.name == sg_name:
- cmsg = sg
- log.debug("Security group '%s' already exists; will add authorizations next." % sg_name)
- break
- # If it does not exist, create security group
- if cmsg is None:
+ Create a security group with all authorizations required to run CloudMan.
+ If the group already exists, check its rules and add the missing ones.
+ Return the name of the created security group.
+ """
+ cm_sg = None
+ # Check if this security group already exists. We can't use the built-in
+ # filtering here, because VPC security groups can't be filtered by name.
+ sg = ec2_conn.get_all_security_groups(filters={'group_name': sg_name})
+ if sg:
+ cm_sg = sg[0]
+ else:
+ # If it does not exist, create security group
log.debug("Creating Security Group %s" % sg_name)
- cmsg = ec2_conn.create_security_group(sg_name, 'A security group for CloudMan')
+ cm_sg = ec2_conn.create_security_group(sg_name, 'A security group for CloudMan', vpc_id=get_or_create_cm_vpc(ec2_conn.access_key, ec2_conn.secret_key).id)
# Add appropriate authorization rules
# If these rules already exist, nothing will be changed in the SG
ports = (('80', '80'), # Web UI
@@ -226,29 +220,68 @@
('30000', '30100'), # FTP transfer
('42284', '42284')) # CloudMan UI
for port in ports:
- try:
- if not rule_exists(cmsg.rules, from_port=port[0], to_port=port[1]):
- cmsg.authorize(ip_protocol='tcp', from_port=port[0], to_port=port[1], cidr_ip='0.0.0.0/0')
- else:
- log.debug("Rule (%s:%s) already exists in the SG" % (port[0], port[1]))
- except EC2ResponseError, e:
- log.error("A problem with security group authorizations: %s" % e)
+ if not rule_exists(cm_sg.rules, from_port=port[0], to_port=port[1]):
+ cm_sg.authorize(ip_protocol='tcp', from_port=port[0], to_port=port[1], cidr_ip='0.0.0.0/0')
+ else:
+ log.debug("Rule (%s:%s) already exists in the SG" % (port[0], port[1]))
# Add rule that allows communication between instances in the same SG
g_rule_exists = False # Flag to indicate if group rule already exists
- for rule in cmsg.rules:
- for grant in rule.grants:
- if grant.name == cmsg.name:
+ for rule in cm_sg.rules:
+ for grant in rule.grants:#[g for g in rule.grants if g.name == cm_sg.name]:
+ print grant.name
+ if grant.name == cm_sg.name:
g_rule_exists = True
log.debug("Group rule already exists in the SG")
if g_rule_exists:
break
- if g_rule_exists is False:
- try:
- cmsg.authorize(src_group=cmsg)
- except EC2ResponseError, e:
- log.error("A problem w/ security group authorization: %s" % e)
- log.info("Done configuring '%s' security group" % cmsg.name)
- return cmsg.name
+ #if g_rule_exists is False:
+ # cm_sg.authorize(src_group=cm_sg)
+ log.info("Done configuring '%s' security group" % cm_sg.name)
+ return cm_sg
+
+
+
+def get_or_create_cm_vpc(a_key, s_key):
+ vpc_conn = boto.vpc.VPCConnection(a_key, s_key)
+ vpcs = vpc_conn.get_all_vpcs()
+ cloudman_vpc = None
+ for vpc in vpcs:
+ if CLOUDMAN_TAG_KEY in vpc.tags:
+ cloudman_vpc = vpc
+ if not cloudman_vpc:
+ #create a new one.
+ cloudman_vpc = vpc_conn.create_vpc('10.0.0.0/16')
+ cloudman_vpc.add_tag(CLOUDMAN_TAG_KEY, '')
+ return cloudman_vpc
+
+
+def get_or_create_cm_subnet(a_key, s_key, availability_zone):
+ log.debug("GETTING SUBNET in %s" % availability_zone)
+ vpc_conn = boto.vpc.VPCConnection(a_key, s_key)
+ subnets = vpc_conn.get_all_subnets()
+ cloudman_subnet = None
+ for subnet in subnets:
+ log.debug("SN: %s, SNAZ:AZ: %s:%s:%s" % (subnet, subnet.availability_zone, availability_zone, subnet.availability_zone == availability_zone))
+ if (not availability_zone or subnet.availability_zone == availability_zone) and CLOUDMAN_TAG_KEY in subnet.tags:
+ cloudman_subnet = subnet
+ if not cloudman_subnet:
+ #create a new one.
+ cloudman_subnet = vpc_conn.create_subnet(get_or_create_cm_vpc(a_key, s_key).id, '10.0.0.0/24', availability_zone)
+ cloudman_subnet.add_tag(CLOUDMAN_TAG_KEY, '')
+ return cloudman_subnet
+
+
+def _format_user_data(cluster_name, key_id, secret, password, share_string, bucket_default):
+ user_provided_data = {'cluster_name': cluster_name,
+ 'access_key': key_id,
+ 'secret_key': secret}
+ if password:
+ user_provided_data['password'] = password
+ if share_string:
+ user_provided_data['share_string'] = share_string
+ if bucket_default:
+ user_provided_data['bucket_default'] = bucket_default
+ return "\n".join(['%s: %s' % (key, value) for key, value in user_provided_data.iteritems() if key != 'kp_material'])
def rule_exists(rules, from_port, to_port, ip_protocol='tcp', cidr_ip='0.0.0.0/0'):
@@ -282,24 +315,22 @@
return kp.name, kp.material
-def run_instance(ec2_conn, user_provided_data, image_id=None,
- kernel_id=None, ramdisk_id=None, key_name=DEFAULT_KEYPAIR,
- placement=None, security_groups=['CloudMan']):
- """ Start an instance. If instance start was OK, return the ResultSet object
- else return None.
+def _run_instance(ec2_conn, user_provided_data, instance_type, image_id=None,
+ kernel_id=None, ramdisk_id=None, key_name=DEFAULT_KEYPAIR,
+ placement=None, security_group_ids=None, subnet_id=None):
+ """
+ Start an instance. If instance start was OK, return the ResultSet object
+ else return None.
"""
rs = None
- instance_type = user_provided_data['instance_type']
- # Remove 'instance_type' key from the dict before creating user data
- del user_provided_data['instance_type']
- ud = "\n".join(['%s: %s' % (key, value) for key, value in user_provided_data.iteritems() if key != 'kp_material'])
try:
rs = ec2_conn.run_instances(image_id=image_id,
instance_type=instance_type,
key_name=key_name,
- security_groups=security_groups,
- user_data=ud,
+ security_group_ids=security_group_ids,
+ user_data=user_provided_data,
kernel_id=kernel_id,
+ subnet_id=subnet_id,
ramdisk_id=ramdisk_id,
placement=placement)
except EC2ResponseError, e:
@@ -312,23 +343,3 @@
else:
log.warning("Problem starting an instance?")
return rs
-
-
-def _find_placement(ec2_conn, instance_type):
- """Find a region zone that supports our requested instance type.
-
- We need to check spot prices in the potential availability zones
- for support before deciding on a region:
-
- http://blog.piefox.com/2011/07/ec2-availability-zones-and-instance.html
- """
- base = ec2_conn.region.name
- yesterday = datetime.datetime.now() - datetime.timedelta(1)
- for loc_choice in ["b", "a", "c", "d"]:
- cur_loc = "{base}{ext}".format(base=base, ext=loc_choice)
- if len(ec2_conn.get_spot_price_history(instance_type=instance_type,
- end_time=yesterday.isoformat(),
- availability_zone=cur_loc)) > 0:
- return cur_loc
- log.error("Did not find availabilty zone in {0} for {1}".format(base, instance_type))
- return None
https://bitbucket.org/galaxy/galaxy-central/commits/347a9169e3ec/
Changeset: 347a9169e3ec
User: dannon
Date: 2014-04-03 21:24:32
Summary: Merge back with -central.
Affected #: 558 files
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -77,6 +77,7 @@
tool-data/shared/ucsc/builds.txt
tool-data/shared/ensembl/builds.txt
tool-data/shared/ucsc/publicbuilds.txt
+tool-data/shared/ucsc/ucsc_build_sites.txt
tool-data/*.loc
tool-data/genome/*
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 README.txt
--- a/README.txt
+++ b/README.txt
@@ -26,6 +26,6 @@
on adding tools can be found on the Galaxy website (linked above).
Not all dependencies are included for the tools provided in the sample
-tool_conf.xml. A full list of external dependencies is available at:
+tool_conf.xml. A full list of external dependencies is available at:
-http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
+https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/Gruntfile.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/Gruntfile.js
@@ -0,0 +1,24 @@
+// NOTE: use 'sudo npm install .', then 'grunt' to use this file
+module.exports = function(grunt) {
+ grunt.initConfig({
+ pkg: grunt.file.readJSON('package.json'),
+ requirejs: {
+ compile: {
+ options: {
+ baseUrl : "../../../../static/scripts/",
+ paths : {
+ "plugin": "../../config/plugins/visualizations/charts/static"
+ },
+ shim : {
+ "libs/underscore": { exports: "_" },
+ "libs/backbone/backbone": { exports: "Backbone" }
+ },
+ name : "plugin/app",
+ out : "static/build-app.js",
+ }
+ }
+ }
+ });
+ grunt.loadNpmTasks('grunt-contrib-requirejs');
+ grunt.registerTask( 'default', [ 'requirejs' ]);
+};
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/package.json
--- /dev/null
+++ b/config/plugins/visualizations/charts/package.json
@@ -0,0 +1,18 @@
+{
+ "name": "galaxy-charts",
+ "version": "0.0.0",
+ "description": "Charts visualization plugin for the Galaxy informatics framework",
+ "main": " ",
+ "keywords": [
+ "galaxy",
+ "visualization",
+ "d3"
+ ],
+ "author": "Aysam Guerler",
+ "license": "BSD",
+ "devDependencies": {
+ "grunt": "~0.4.1",
+ "grunt-cli": "~0.1.9",
+ "grunt-contrib-requirejs": "~0.4.3"
+ }
+}
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -1,10 +1,12 @@
// dependencies
-define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils',
- 'plugin/views/charts', 'plugin/views/viewport', 'plugin/views/chart', 'plugin/views/group',
- 'plugin/models/config', 'plugin/models/datasets', 'plugin/models/chart', 'plugin/models/charts', 'plugin/models/group', 'plugin/models/types'],
- function( Portlet, Ui, Utils,
- ChartsView, ViewportView, ChartView, GroupView,
- Config, Datasets, Chart, Charts, Group, Types
+define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils',
+ 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage',
+ 'plugin/views/viewer', 'plugin/views/editor',
+ 'plugin/models/config', 'plugin/models/chart',
+ 'plugin/charts/types'],
+ function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage,
+ ViewerView, EditorView,
+ Config, Chart, Types
) {
// widget
@@ -13,66 +15,75 @@
// initialize
initialize: function(options)
{
+ // deactivate all debugs outputs
+ //window.console.debug = function() {};
+
// link options
this.options = options;
- // link galaxy
- this.modal = parent.Galaxy.modal;
+ // link galaxy modal or create one
+ if (Galaxy && Galaxy.modal) {
+ this.modal = Galaxy.modal;
+ } else {
+ this.modal = new Modal.View();
+ }
- // create configuration model
+ //
+ // models
+ //
this.config = new Config();
-
- // create chart models
this.types = new Types();
this.chart = new Chart();
- this.charts = new Charts();
- this.group = new Group();
- // create dataset handler
+ //
+ // libraries
+ //
+ this.jobs = new Jobs(this);
this.datasets = new Datasets(this);
+ this.storage = new Storage(this);
- // create views
- this.charts_view = new ChartsView(this);
- this.group_view = new GroupView(this);
- this.chart_view = new ChartView(this);
- this.viewport_view = new ViewportView(this);
-
- // append view port to charts viewer
- this.charts_view.append(this.viewport_view.$el);
-
- // create portlet
- if (!this.options.config.widget) {
- this.portlet = new Portlet.View({icon : 'fa-bar-chart-o', title : 'Charts'});
- } else {
- this.portlet = $('<div></div>');
- }
+ //
+ // views
+ //
+ this.viewer_view = new ViewerView(this);
+ this.editor_view = new EditorView(this);
// append views
- this.portlet.append(this.charts_view.$el);
- this.portlet.append(this.group_view.$el);
- this.portlet.append(this.chart_view.$el);
-
- // set element
- if (!this.options.config.widget) {
- this.setElement(this.portlet.$el);
+ this.$el.append(this.viewer_view.$el);
+ this.$el.append(this.editor_view.$el);
+
+ // pick start screen
+ if (!this.storage.load()) {
+ // show editor
+ this.go('editor');
} else {
- this.setElement(this.portlet);
+ // show viewport
+ this.go('viewer');
+
+ // draw chart
+ var self = this;
+ this.chart.deferred.execute(function() {
+ self.chart.trigger('redraw');
+ });
}
-
- // hide views
- this.group_view.$el.hide();
- this.charts_view.$el.hide();
-
- // events
- var self = this;
- this.config.on('change:current_view', function() {
- self._showCurrent();
- });
},
- // current view
- _showCurrent: function() {
+ // loads a view and makes sure that all others are hidden
+ go: function(view_id) {
+ // hide all tooltips
+ $('.tooltip').hide();
+ // pick view
+ switch (view_id) {
+ case 'editor' :
+ this.editor_view.show();
+ this.viewer_view.hide();
+ break;
+ case 'viewer' :
+ this.editor_view.hide();
+ this.viewer_view.show();
+ break;
+ }
},
// execute command
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/build-app.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -0,0 +1,6 @@
+// Underscore.js 1.4.4
+// http://underscorejs.org
+// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore may be freely distributed under the MIT license.
+
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options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"chartskit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:a,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the Charts-Kit. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh")},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._create_svg();var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_create_svg:function(){this.svg&&this.svg.remove(),this.$el.append($(this._template_svg())),this.svg_el=this.$el.find("svg"),this.svg=d3.select(this.svg_el[0])},_draw:function(e){var t=this;this._create_svg(),e.state("wait","Please wait...");var n=e.deferred.register(),r=e.get("type"),i=this.app.types.get(r);if(!i.execute||i.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var s=new r(t.app,{svg:t.svg});i.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){s.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):s.draw(n,e,t._defaultRequestDictionary(e)):s.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={groups:[]};t.execute?n.id=e.get("dataset_id_job"):n.id=e.get("dataset_id");var r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n},_template:function(){return'<div style="height: 100%; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_svg:function(){return'<svg style="height: calc(100% - 80px)"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Customize",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("wait","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/_nvd3/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/_nvd3/config.js
@@ -0,0 +1,218 @@
+define([], function() {
+
+return {
+ title : '',
+ columns : {
+ y : {
+ title : 'Values for y-axis'
+ }
+ },
+ settings : {
+ separator_label : {
+ title : 'X axis',
+ type : 'separator'
+ },
+ x_axis_label : {
+ title : 'Axis label',
+ info : 'Provide a label for the axis.',
+ type : 'text',
+ init : 'X-axis',
+ placeholder : 'Axis label'
+ },
+ x_axis_type : {
+ title : 'Axis value type',
+ info : 'Select the value type of the axis.',
+ type : 'select',
+ init : 'auto',
+ data : [
+ {
+ label : '-- Do not show values --',
+ value : 'hide',
+ hide : 'x_axis_tick'
+ },
+ {
+ label : 'Auto',
+ value : 'auto',
+ hide : 'x_axis_tick'
+ },
+ {
+ label : 'Float',
+ value : 'f',
+ show : 'x_axis_tick'
+ },
+ {
+ label : 'Exponent',
+ value : 'e',
+ show : 'x_axis_tick'
+ },
+ {
+ label : 'Integer',
+ value : 'd',
+ hide : 'x_axis_tick'
+ },
+ {
+ label : 'Percentage',
+ value : 'p',
+ show : 'x_axis_tick'
+ },
+ {
+ label : 'Rounded',
+ value : 'r',
+ show : 'x_axis_tick'
+ },
+ {
+ label : 'SI-prefix',
+ value : 's',
+ show : 'x_axis_tick'
+ }
+ ]
+ },
+ x_axis_tick : {
+ title : 'Axis tick format',
+ info : 'Select the tick format for the axis.',
+ type : 'select',
+ init : '.1',
+ data : [
+ {
+ label : '0.00001',
+ value : '.5'
+ },
+ {
+ label : '0.0001',
+ value : '.4'
+ },
+ {
+ label : '0.001',
+ value : '.3'
+ },
+ {
+ label : '0.01',
+ value : '.2'
+ },
+ {
+ label : '0.1',
+ value : '.1'
+ },
+ {
+ label : '1',
+ value : '1'
+ }
+ ]
+
+ },
+ separator_tick : {
+ title : 'Y axis',
+ type : 'separator'
+ },
+ y_axis_label : {
+ title : 'Axis label',
+ info : 'Provide a label for the axis.',
+ type : 'text',
+ init : 'Y-axis',
+ placeholder : 'Axis label'
+ },
+ y_axis_type : {
+ title : 'Axis value type',
+ info : 'Select the value type of the axis.',
+ type : 'select',
+ init : 'auto',
+ data : [
+ {
+ label : '-- Do not show values --',
+ value : 'hide',
+ hide : 'y_axis_tick'
+ },
+ {
+ label : 'Auto',
+ value : 'auto',
+ hide : 'y_axis_tick'
+ },
+ {
+ label : 'Float',
+ value : 'f',
+ show : 'y_axis_tick'
+ },
+ {
+ label : 'Exponent',
+ value : 'e',
+ show : 'y_axis_tick'
+ },
+ {
+ label : 'Integer',
+ value : 'd',
+ hide : 'y_axis_tick'
+ },
+ {
+ label : 'Percentage',
+ value : 'p',
+ show : 'y_axis_tick'
+ },
+ {
+ label : 'Rounded',
+ value : 'r',
+ show : 'y_axis_tick'
+ },
+ {
+ label : 'SI-prefix',
+ value : 's',
+ show : 'y_axis_tick'
+ }
+ ]
+ },
+ y_axis_tick : {
+ title : 'Axis tick format',
+ info : 'Select the tick format for the axis.',
+ type : 'select',
+ init : '.1',
+ data : [
+ {
+ label : '0.00001',
+ value : '.5'
+ },
+ {
+ label : '0.0001',
+ value : '.4'
+ },
+ {
+ label : '0.001',
+ value : '.3'
+ },
+ {
+ label : '0.01',
+ value : '.2'
+ },
+ {
+ label : '0.1',
+ value : '.1'
+ },
+ {
+ label : '1',
+ value : '1'
+ }
+ ]
+
+ },
+ separator_legend : {
+ title : 'Others',
+ type : 'separator'
+ },
+ show_legend : {
+ title : 'Show legend',
+ info : 'Would you like to add a legend?',
+ type : 'select',
+ init : 'true',
+ data : [
+ {
+ label : 'Yes',
+ value : 'true'
+ },
+ {
+ label : 'No',
+ value : 'false'
+ }
+ ]
+ },
+ }
+};
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
@@ -0,0 +1,80 @@
+// dependencies
+define([], function() {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, nvd3_model, chart, request_dictionary, callback)
+ {
+ // request data
+ var self = this;
+ this.app.datasets.request(request_dictionary, function(data) {
+ nv.addGraph(function() {
+ // x axis
+ self._axis(nvd3_model.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick'));
+
+ // x axis label
+ nvd3_model.xAxis.axisLabel(chart.settings.get('x_axis_label'));
+
+ // y axis
+ self._axis(nvd3_model.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick'));
+
+ // y axis label
+ nvd3_model.yAxis.axisLabel(chart.settings.get('y_axis_label'))
+ .axisLabelDistance(30);
+
+ // controls
+ if (chart.groups.length == 1) {
+ nvd3_model.options({ showControls: false });
+ }
+
+ // legend
+ var legend_visible = true;
+ if (chart.settings.get('show_legend') == 'false') {
+ legend_visible = false;
+ }
+ nvd3_model.showLegend(legend_visible);
+
+ // custom callback
+ if (callback) {
+ callback(nvd3_model);
+ }
+
+ // parse data to svg
+ self.options.svg.datum(data)
+ .call(nvd3_model);
+
+ // refresh on window resize
+ nv.utils.windowResize(nvd3_model.update);
+
+ // set chart state
+ chart.state('ok', 'Chart has been drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ });
+ });
+ },
+
+ // make axis
+ _axis: function(axis, type, tick) {
+ switch (type) {
+ case 'hide':
+ axis.tickFormat(function() { return '' });
+ break;
+ case 'auto':
+ break;
+ default:
+ axis.tickFormat(d3.format(tick + type));
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/bardiagram.js
--- a/config/plugins/visualizations/charts/static/charts/bardiagram.js
+++ /dev/null
@@ -1,33 +0,0 @@
-// dependencies
-define([], function() {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- refresh : function(data)
- {
- // add graph to screen
- var self = this;
- nv.addGraph(function() {
- self.d3_chart = nv.models.multiBarChart();
-
- self.d3_chart.xAxis.tickFormat(d3.format('.2f'))
- self.d3_chart.yAxis.tickFormat(d3.format('.1f'))
-
- d3.select(self.options.svg_id)
- .datum(data)
- .call(self.d3_chart);
-
- nv.utils.windowResize(self.d3_chart.update);
- });
- }
-});
-
-});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/bardiagram/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/bardiagram/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Bar diagram',
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/histogram/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/histogram/config.js
@@ -0,0 +1,21 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Histogram',
+ execute : true,
+ columns : {
+ y : {
+ title : 'Observations'
+ }
+ },
+ settings : {
+ x_axis_label : {
+ init : 'Breaks'
+ },
+ y_axis_label : {
+ init : 'Density'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/histogram/histogram.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/histogram/histogram.js
@@ -0,0 +1,31 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // configure request
+ var index = 0;
+ for (var i in request_dictionary.groups) {
+ var group = request_dictionary.groups[i];
+ group.columns = {
+ x: index++,
+ y: index++
+ }
+ }
+
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/horizontal.js
--- a/config/plugins/visualizations/charts/static/charts/horizontal.js
+++ /dev/null
@@ -1,33 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- this.chart = options.chart;
- },
-
- // render
- refresh : function(data)
- {
- // add graph to screen
- var self = this;
- nv.addGraph(function() {
- self.d3_chart = nv.models.multiBarHorizontalChart();
-
- self.d3_chart.xAxis.tickFormat(function() { return ''; });
-
- d3.select(self.options.svg_id)
- .datum(data)
- .call(self.d3_chart);
-
- nv.utils.windowResize(self.d3_chart.update);
- });
- }
-});
-
-});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/horizontal/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/horizontal/config.js
@@ -0,0 +1,12 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Bar diagram (horizontal)',
+ settings : {
+ x_axis_type : {
+ init : 'hide'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/line.js
--- a/config/plugins/visualizations/charts/static/charts/line.js
+++ /dev/null
@@ -1,39 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- this.chart = options.chart;
- },
-
- // render
- refresh : function(data)
- {
- // add graph to screen
- var self = this;
- nv.addGraph(function() {
- self.chart_3d = nv.models.lineChart();
-
- self.chart_3d.xAxis
- .tickFormat(d3.format(',f'));
-
- self.chart_3d.yAxis
- .tickFormat(d3.format(',.2f'));
-
- d3.select(self.options.svg_id)
- .datum(data)
- .call(self.chart_3d);
-
- nv.utils.windowResize(self.chart_3d.update);
-
- return self.chart_3d;
- });
- }
-});
-
-});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/line/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/line/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Line chart',
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/line/line.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/line/line.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/linewithfocus.js
--- a/config/plugins/visualizations/charts/static/charts/linewithfocus.js
+++ /dev/null
@@ -1,37 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- this.chart = options.chart;
- },
-
- // render
- refresh : function(data)
- {
- // add graph to screen
- var self = this;
- nv.addGraph(function() {
- self.chart_3d = nv.models.lineWithFocusChart();
-
- self.chart_3d.xAxis
- .tickFormat(d3.format(',f'));
-
- self.chart_3d.yAxis
- .tickFormat(d3.format(',.2f'));
-
- d3.select(self.options.svg_id)
- .datum(data)
- .call(self.chart_3d);
-
- nv.utils.windowResize(self.chart_3d.update);
- });
- }
-});
-
-});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/linewithfocus/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/linewithfocus/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Line with focus',
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/piechart.js
--- a/config/plugins/visualizations/charts/static/charts/piechart.js
+++ /dev/null
@@ -1,51 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- this.chart = options.chart;
- },
-
- // render
- refresh : function(data)
- {
- // loop through data groups
- for (var key in data) {
- // get group
- var group = data[key];
-
- // format chart data
- var pie_data = [];
- for (var key in group.values) {
- var value = group.values[key];
- pie_data.push ({
- key : value.x,
- y : value.y
- });
- }
-
- // add graph to screen
- var self = this;
- nv.addGraph(function() {
- self.chart_3d = nv.models.pieChart()
- .donut(true)
- .showLegend(false);
-
- d3.select(self.options.svg_id)
- .datum(pie_data)
- .call(self.chart_3d);
-
- nv.utils.windowResize(self.chart_3d.update);
-
- return self.chart_3d;
- });
- }
- }
-});
-
-});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/piechart/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/piechart/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Pie chart',
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/piechart/piechart.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/piechart/piechart.js
@@ -0,0 +1,57 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // request data
+ var self = this;
+ this.app.datasets.request(request_dictionary, function(data) {
+
+ // loop through data groups
+ for (var key in request_dictionary.groups) {
+ // get group
+ var group = request_dictionary.groups[key];
+
+ // format chart data
+ var pie_data = [];
+ for (var key in group.values) {
+ var value = group.values[key];
+ pie_data.push ({
+ key : value.x,
+ y : value.y
+ });
+ }
+
+ // add graph to screen
+ nv.addGraph(function() {
+ self.chart_3d = nv.models.pieChart()
+ .donut(true)
+ .showLegend(false);
+
+ self.options.svg.datum(pie_data)
+ .call(self.chart_3d);
+
+ nv.utils.windowResize(self.chart_3d.update);
+
+ // set chart state
+ chart.state('ok', 'Pie chart drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ });
+ }
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/scatterplot.js
--- a/config/plugins/visualizations/charts/static/charts/scatterplot.js
+++ /dev/null
@@ -1,37 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- this.chart = options.chart;
- },
-
- // render
- refresh : function(data)
- {
- // add graph to screen
- var self = this;
- nv.addGraph(function() {
- self.d3_chart = nv.models.scatterChart()
- .showDistX(true)
- .showDistY(true)
- .color(d3.scale.category10().range());
-
- self.d3_chart.xAxis.tickFormat(d3.format('.02f'))
- self.d3_chart.yAxis.tickFormat(d3.format('.02f'))
-
- d3.select(self.options.svg_id)
- .datum(data)
- .call(self.d3_chart);
-
- nv.utils.windowResize(self.d3_chart.update);
- });
- }
-});
-
-});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/scatterplot/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/scatterplot/config.js
@@ -0,0 +1,12 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Scatter plot',
+ columns : {
+ x : {
+ title : 'Values for x-axis'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/scatterplot/scatterplot.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/scatterplot/scatterplot.js
@@ -0,0 +1,25 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.scatterChart(), chart, request_dictionary, function(nvd3_model) {
+ nvd3_model.showDistX(true)
+ .showDistY(true)
+ .color(d3.scale.category10().range());
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/stackedarea.js
--- a/config/plugins/visualizations/charts/static/charts/stackedarea.js
+++ /dev/null
@@ -1,59 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- this.chart = options.chart;
- },
-
- // render
- refresh : function(data)
- {
- // add graph to screen
- var self = this;
- nv.addGraph(function() {
- // check data
- var valid = true;
- var length = 0;
- for (var key in data) {
- // evalute length
- if (length == 0) {
- length = data[key].values.length;
- } else {
- if (length != data[key].values.length) {
- valid = false;
- break;
- }
- }
- }
- if (!valid) {
- return;
- }
-
- // make plot
- self.d3_chart = nv.models.stackedAreaChart()
- .x(function(d) {
- return d.x
- })
- .y(function(d) {
- return d.y
- })
- .clipEdge(true);
-
- self.d3_chart.xAxis.tickFormat(function() { return ''; });
-
- d3.select(self.options.svg_id)
- .datum(data)
- .call(self.d3_chart);
-
- nv.utils.windowResize(self.d3_chart.update);
- });
- }
-});
-
-});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/stackedarea/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/stackedarea/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Stacked area'
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/stackedarea/stackedarea.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/stackedarea/stackedarea.js
@@ -0,0 +1,26 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) {
+ // make plot
+ nvd3_model.x(function(d) { return d.x })
+ .y(function(d) { return d.y })
+ .clipEdge(true);
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/charts/types.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/types.js
@@ -0,0 +1,39 @@
+// dependencies
+define(['plugin/charts/bardiagram/config',
+ //'plugin/charts/boxplot/config',
+ 'plugin/charts/histogram/config',
+ 'plugin/charts/horizontal/config',
+ 'plugin/charts/line/config',
+ 'plugin/charts/linewithfocus/config',
+ 'plugin/charts/piechart/config',
+ 'plugin/charts/scatterplot/config',
+ 'plugin/charts/stackedarea/config',
+ ], function(bardiagram,
+ //boxplot,
+ histogram,
+ horizontal,
+ line,
+ linewithfocus,
+ piechart,
+ scatterplot,
+ stackedarea
+ ) {
+
+// widget
+return Backbone.Model.extend(
+{
+ // types
+ defaults: {
+ 'bardiagram' : bardiagram,
+ //'boxplot' : boxplot,
+ 'horizontal' : horizontal,
+ 'histogram' : histogram,
+ 'line' : line,
+ 'linewithfocus' : linewithfocus,
+ 'piechart' : piechart,
+ 'scatterplot' : scatterplot,
+ 'stackedarea' : stackedarea
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/library/datasets.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/library/datasets.js
@@ -0,0 +1,149 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.Collection.extend(
+{
+ // list of datasets
+ list: {},
+
+ // initialize
+ initialize: function(app, options)
+ {
+ // link app
+ this.app = app;
+
+ // configure options
+ this.options = Utils.merge(options, this.optionsDefault);
+ },
+
+ // wait
+ request: function(options, success, error) {
+ // link this
+ var self = this;
+
+ // check if column data is requested
+ if (options.groups) {
+ this._fetch(options, success);
+ } else {
+ // check if dataset is available from cache
+ var dataset = this.list[options.id];
+ if (dataset) {
+ success(dataset);
+ return;
+ }
+
+ // request dataset
+ Utils.request('GET', config.root + 'api/datasets/' + options.id, {}, function(dataset) {
+ switch (dataset.state) {
+ case 'error':
+ if (error) {
+ error(dataset);
+ }
+ break;
+ default:
+ self.list[options.id] = dataset;
+ success(dataset);
+ }
+ });
+ }
+ },
+
+ // fetch data columns into dataset object
+ _fetch: function(options, callback) {
+ // set offset
+ var offset = options.start ? options.start : 0;
+
+ // set limit
+ var limit = Math.abs(options.end - options.start);
+ var query_limit = this.app.config.get('query_limit');
+ if (!limit || limit > query_limit) {
+ limit = query_limit;
+ }
+
+ // get column indices
+ var index_string = '';
+ var index_map = {};
+ var index_count = 0;
+ for (var i in options.groups) {
+ var group = options.groups[i];
+ for (var key in group.columns) {
+ var column = group.columns[key];
+
+ // add to index string
+ index_string += column + ',';
+
+ // add to dictionary
+ index_map[column] = index_count;
+
+ // increase counter
+ index_count++;
+ }
+ }
+ if (index_count == 0) {
+ callback({});
+ return;
+ }
+ index_string = index_string.substring(0, index_string.length - 1);
+
+ // initialize result dictionary
+ var result = options.groups.slice(0);
+ for (var i in result) {
+ result[i].values = [];
+ }
+
+ // make request
+ var self = this;
+ Utils.request('GET', config.root + 'api/datasets/' + options.id, {
+ data_type : 'raw_data',
+ provider : 'dataset-column',
+ limit : limit,
+ offset : offset,
+ indeces : index_string
+ }, function(response) {
+
+ // loop through rows
+ for (var i in response.data) {
+ // get row
+ var row = response.data[i];
+
+ // collect all data into the defined groups
+ for (var j in options.groups) {
+ // get group
+ var group = options.groups[j];
+
+ // initialize value
+ var value = {
+ x : parseInt(i) + offset
+ };
+
+ // fill value
+ for (var key in group.columns) {
+ // get column
+ var column = group.columns[key];
+
+ // identify column
+ var index = index_map[column];
+
+ // read value from row
+ var v = row[index];
+ if(isNaN(v) || !v) {
+ v = 0;
+ }
+
+ // add value to dictionary
+ value[key] = v;
+ }
+
+ // add to result
+ result[j].values.push(value);
+ }
+ }
+
+ // callback
+ callback(result);
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/library/deferred.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/library/deferred.js
@@ -0,0 +1,85 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// deferred process handler
+return Backbone.Model.extend(
+{
+ // queue
+ queue: [],
+
+ // list of currently registered processes
+ process: {},
+
+ // process counter
+ counter: 0,
+
+ // initialize
+ initialize: function()
+ {
+ // loop through queue and check states
+ this.on('refresh', function() {
+ if (this.counter == 0) {
+ for (var index in this.queue) {
+ // execute callback
+ this.queue[index]();
+
+ // remove callback
+ this.queue.splice(index, 1);
+ }
+ }
+ });
+ },
+
+ // executes callback once all processes are unregistered
+ execute: function(callback) {
+ // add wrapper to queue
+ this.queue.push(callback);
+
+ // trigger change
+ this.trigger('refresh');
+ },
+
+ // register process
+ register: function() {
+ // create unique id
+ var id = Utils.uuid();
+
+ // add process to queue
+ this.process[id] = true;
+
+ // increase process counter
+ this.counter++;
+
+ // log
+ console.debug('Deferred:register() - Registering ' + id);
+
+ // return unique id
+ return id;
+ },
+
+ // unregister process
+ done: function(id) {
+ // delete tag
+ delete this.process[id];
+
+ // decrease process counter
+ this.counter--;
+
+ // log
+ console.debug('Deferred:done() - Unregistering ' + id);
+
+ // trigger change
+ this.trigger('refresh');
+ },
+
+ // ready
+ ready: function() {
+ if (this.counter == 0) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/library/jobs.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -0,0 +1,152 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.Model.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ // link app
+ this.app = app;
+
+ // link options
+ this.options = Utils.merge(options, this.optionsDefault);
+ },
+
+ // clean
+ cleanup: function(chart) {
+ // cleanup previous dataset file
+ var previous = chart.get('dataset_id_job');
+ if (previous != '') {
+ var self = this;
+ Utils.request('PUT', config.root + 'api/histories/none/contents/' + previous, { deleted: true }, function() {
+ // update galaxy history
+ self._refreshHdas();
+ });
+
+ // reset id
+ chart.set('dataset_id_job', '');
+ }
+ },
+
+ // create job
+ submit: function(chart, settings_string, columns_string, success, error) {
+ // link this
+ var self = this;
+
+ // backup chart details
+ var chart_id = chart.id;
+ var chart_type = chart.get('type');
+
+ // get chart settings
+ var chart_settings = this.app.types.get(chart_type);
+
+ // configure tool
+ data = {
+ 'tool_id' : 'chartskit',
+ 'inputs' : {
+ 'input' : {
+ 'id' : chart.get('dataset_id'),
+ 'src' : 'hda'
+ },
+ 'module' : chart_type,
+ 'columns' : columns_string,
+ 'settings' : settings_string
+ }
+ }
+
+ // set chart state
+ chart.state('wait', 'Sending job request...');
+
+ // post job
+ Utils.request('POST', config.root + 'api/tools', data,
+ // success handler
+ function(response) {
+ if (!response.outputs || response.outputs.length == 0) {
+ chart.state('failed', 'Job submission failed. No response.');
+
+ // call error
+ error && error();
+ } else {
+ // update galaxy history
+ self._refreshHdas();
+
+ // get dataset
+ var job = response.outputs[0];
+
+ // check dataset
+ chart.state('wait', 'Job has been queued...');
+
+ // backup resulting dataset id
+ chart.set('dataset_id_job', job.id);
+
+ // save
+ this.app.storage.save();
+
+ // wait for job completion
+ self._loop(job.id, function(job) {
+ switch (job.state) {
+ case 'ok':
+ // update state
+ chart.state('wait', 'Job completed successfully...');
+
+ // execute success
+ success(job);
+
+ // stop loop
+ return true;
+ case 'error':
+ // update state
+ chart.state('failed', 'Job has failed. Please check the history for details.');
+
+ // call error
+ error && error();
+
+ // stop loop
+ return true;
+ case 'running':
+ // wait
+ chart.state('wait', 'Job is running...');
+
+ // continue loop
+ return false;
+ }
+ });
+ }
+ },
+ // error handler
+ function(response) {
+ var message = '';
+ if (response && response.message && response.message.data && response.message.data.input) {
+ message = response.message.data.input + '.';
+ }
+ // update state
+ chart.state('failed', 'This visualization requires the Charts-Kit. Please make sure it is installed. ' + message);
+
+ // call error
+ error && error();
+
+ }
+ );
+ },
+
+ // request job details
+ _loop: function(id, callback) {
+ var self = this;
+ Utils.request('GET', config.root + 'api/jobs/' + id, {}, function(job) {
+ if (!callback(job)) {
+ setTimeout(function() { self._loop(id, callback); }, self.app.config.get('query_timeout'));
+ }
+ });
+ },
+
+ // refresh history panel
+ _refreshHdas: function() {
+ // update galaxy history
+ if (Galaxy && Galaxy.currHistoryPanel) {
+ Galaxy.currHistoryPanel.refreshHdas();
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r e45c2616e207e25e4978d14343bd5bff495a16b0 -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 config/plugins/visualizations/charts/static/library/storage.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/library/storage.js
@@ -0,0 +1,120 @@
+// dependencies
+define(['utils/utils', 'plugin/models/chart', 'plugin/models/group'], function(Utils, Chart, Group) {
+
+// collection
+return Backbone.Model.extend(
+{
+ // viz model
+ vis: null,
+
+ // initialize
+ initialize: function(app) {
+ // link app
+ this.app = app;
+
+ // link chart
+ this.chart = this.app.chart;
+
+ // link options
+ this.options = this.app.options;
+
+ // initialize parameters
+ this.id = this.options.id;
+
+ // create visualization
+ this.vis = new Visualization({
+ type : 'charts',
+ config : {
+ dataset_id : this.options.config.dataset_id,
+ chart_dict : {}
+ }
+ });
+
+ // add visualization id
+ if (this.id) {
+ this.vis.id = this.id;
+ }
+
+ // add charts
+ var chart_dict = this.options.config.chart_dict;
+ if (chart_dict) {
+ this.vis.get('config').chart_dict = chart_dict;
+ }
+ },
+
+ // pack and save nested chart model
+ save: function() {
+
+ // link chart
+ var chart = this.app.chart;
+
+ // reset
+ this.vis.get('config').chart_dict = {};
+
+ // set title
+ var title = chart.get('title');
+ if (title != '') {
+ this.vis.set('title', title);
+ }
+
+ // create chart dictionary
+ var chart_dict = {
+ attributes : chart.attributes,
+ settings : chart.settings.attributes,
+ groups : []
+ };
+
+ // append groups
+ chart.groups.each(function(group) {
+ chart_dict.groups.push(group.attributes);
+ });
+
+ // add chart to charts array
+ this.vis.get('config').chart_dict = chart_dict;
+
+ // save visualization
+ var self = this;
+ this.vis.save()
+ .fail(function(xhr, status, message) {
+ console.error(xhr, status, message);
+ })
+ .then(function(response) {
+ if (response && response.id) {
+ self.id = response.id;
+ }
+ });
+ },
+
+ // load nested models/collections from packed dictionary
+ load: function() {
+ // get charts array
+ var chart_dict = this.vis.get('config').chart_dict;
+
+ // check
+ if (!chart_dict.attributes) {
+ return false;
+ }
+
+ // main
+ this.chart.set(chart_dict.attributes);
+
+ // set state
+ this.chart.state('ok', 'Loading saved visualization...');
+
+ // get settings
+ this.chart.settings.set(chart_dict.settings);
+
+ // get groups
+ for (var j in chart_dict.groups) {
+ this.chart.groups.add(new Group(chart_dict.groups[j]));
+ }
+
+ // reset modified flag
+ this.chart.set('modified', false);
+
+ // return
+ return true;
+ }
+});
+
+});
\ No newline at end of file
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/galaxy/galaxy-central/commits/19e8344a0497/
Changeset: 19e8344a0497
User: dannon
Date: 2014-04-21 23:10:23
Summary: Convert cloudlaunch over to bioblend egg/launching, unifying the two approaches. The bioblend codebase will be where improvements (vpc, etc) happen moving forward.
Affected #: 3 files
diff -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -35,6 +35,7 @@
amqp = 1.4.3
anyjson = 0.3.3
Beaker = 1.4
+bioblend = 0.4.2
boto = 2.27.0
decorator = 3.1.2
docutils = 0.7
diff -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -16,16 +16,16 @@
from galaxy.util.json import to_json_string
eggs.require('boto')
-import boto
-import boto.vpc
-from boto.ec2.regioninfo import RegionInfo
-from boto.exception import EC2ResponseError, S3ResponseError
-from boto.s3.connection import OrdinaryCallingFormat, S3Connection
+eggs.require('bioblend')
+eggs.require('pyyaml')
+
+from boto.exception import EC2ResponseError
+
+
+from bioblend import cloudman
log = logging.getLogger(__name__)
-logging.getLogger('boto').setLevel(logging.INFO)
-
PKEY_PREFIX = 'gxy_pkey'
DEFAULT_KEYPAIR = 'cloudman_keypair'
@@ -55,71 +55,29 @@
Get EC2 Account Info
"""
account_info = {}
- try:
- ec2_conn = connect_ec2(key_id, secret)
- kps = ec2_conn.get_all_key_pairs()
- except EC2ResponseError, e:
- log.error("Problem starting an instance: %s\n%s" % (e, e.body))
- trans.response.status = 400
- return e.error_message or "Error retrieving account information. Please verify your credentials are correct, and contact galaxy support to report this issue."
+ cml = cloudman.launch.CloudManLauncher(key_id, secret)
+ ec2_conn = cml.connect_ec2(key_id, secret)
+ kps = ec2_conn.get_all_key_pairs()
+ account_info['clusters'] = cml.get_clusters_pd()
account_info['keypairs'] = [akp.name for akp in kps]
- #Existing Clusters
- s3_conn = S3Connection(key_id, secret, calling_format=OrdinaryCallingFormat())
- buckets = s3_conn.get_all_buckets()
- clusters = []
- for bucket in buckets:
- try:
- pd = bucket.get_key('persistent_data.yaml')
- except S3ResponseError, e:
- # This can fail for a number of reasons for non-us and/or CNAME'd buckets.
- log.error("Problem fetching persistent_data.yaml from bucket: %s \n%s" % (e, e.body))
- continue
- if pd:
- # This is a cloudman bucket.
- # We need to get persistent data, and the cluster name.
- # DBTODO: Add pyyaml egg, and rewrite this.
- # This will also allow for much more sophisticated rendering of existing clusters
- # Currently, this zone detection is a hack.
- pd_contents = pd.get_contents_as_string()
- zone = get_zone_from_pd(pd_contents, ec2_conn)
- for key in bucket.list():
- if key.name.endswith('.clusterName'):
- clusters.append({'name': key.name.split('.clusterName')[0],
- 'persistent_data': pd_contents,
- 'zone': zone})
- account_info['clusters'] = clusters
- account_info['zones'] = [z.name for z in ec2_conn.get_all_zones()]
return to_json_string(account_info)
@web.expose
- def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=None, zone=None, bucket_default=None, **kwargs):
- ec2_error = None
- try:
- # Create security group & key pair used when starting an instance
- ec2_conn = connect_ec2(key_id, secret)
- sg = get_or_create_cm_security_group(ec2_conn)
- kp_name, kp_material = create_key_pair(ec2_conn, key_name=keypair)
- except EC2ResponseError, err:
- ec2_error = err.error_message
- if ec2_error:
- trans.response.status = 400
- return ec2_error
- #Get an elastic ip, add to UserData.
- user_provided_data = _format_user_data(cluster_name, key_id, secret, password, share_string, bucket_default)
- if not ami:
- ami = trans.app.config.cloudlaunch_default_ami
- rs = _run_instance(ec2_conn=ec2_conn,
- image_id=ami,
- user_provided_data=user_provided_data,
- key_name=kp_name,
- security_group_ids=[sg.id],
- placement=zone,
- instance_type=instance_type,
- subnet_id=get_or_create_cm_subnet(key_id, secret, zone).id)
- if not rs:
+ def launch_instance(self, trans, cluster_name, password, key_id, secret,
+ instance_type, share_string, keypair, ami=None,
+ zone=None, bucket_default=None, **kwargs):
+ ami = ami or trans.app.config.cloudlaunch_default_ami
+ cfg = cloudman.CloudManConfig(key_id, secret, cluster_name, ami,
+ instance_type, password, placement=zone)
+ cml = cloudman.launch.CloudManLauncher(key_id, secret)
+ result = cml.launch(cluster_name, ami, instance_type, password,
+ cfg.kernel_id, cfg.ramdisk_id, cfg.key_name,
+ cfg.security_groups, cfg.placement)
+ #result is a dict with sg_names, kp_name, kp_material, rs, and instance_id
+ if not result['rs']:
trans.response.status = 400
return "Instance failure, but no specific error was detected. Please check your AWS Console."
- instance = rs.instances[0]
+ instance = result['rs'].instances[0]
while not instance.public_dns_name:
try:
instance.update()
@@ -127,20 +85,20 @@
# This can happen when update is invoked before the instance is fully registered.
pass
time.sleep(1)
- if kp_material:
+ if result['kp_material']:
#We have created a keypair. Save to tempfile for one time retrieval.
(fd, fname) = tempfile.mkstemp(prefix=PKEY_PREFIX, dir=trans.app.config.new_file_path)
f = os.fdopen(fd, 'wt')
- f.write(kp_material)
+ f.write(result['kp_material'])
f.close()
kp_material_tag = fname[fname.rfind(PKEY_PREFIX) + len(PKEY_PREFIX):]
else:
kp_material_tag = None
return to_json_string({'cluster_name': cluster_name,
- 'instance_id': rs.instances[0].id,
- 'image_id': rs.instances[0].image_id,
- 'public_dns_name': rs.instances[0].public_dns_name,
- 'kp_name': kp_name,
+ 'instance_id': result['rs'].instances[0].id,
+ 'image_id': result['rs'].instances[0].image_id,
+ 'public_dns_name': result['rs'].instances[0].public_dns_name,
+ 'kp_name': result['kp_name'],
'kp_material_tag': kp_material_tag})
@web.expose
@@ -158,188 +116,3 @@
return kp_material
trans.response.status = 400
return "Invalid identifier"
-
-
-def get_zone_from_pd(pd_contents, ec2_conn):
- try:
- for line in pd_contents.split('\n'):
- if 'vol_id' in line:
- vol_id = line.split(':')[1].strip()
- v = ec2_conn.get_all_volumes(volume_ids=[vol_id])
- if v:
- return v[0].zone
- except:
- # Things can go wrong with Zone detection outside of our control. Use
- # the default zone if this happens.
- pass
- return ''
-
-
-def connect_ec2(a_key, s_key):
- """
- Create and return an EC2 connection object.
- """
- # Use variables for forward looking flexibility
- # AWS connection values
- region_name = 'us-east-1'
- region_endpoint = 'ec2.amazonaws.com'
- is_secure = True
- ec2_port = None
- ec2_conn_path = '/'
- r = RegionInfo(name=region_name, endpoint=region_endpoint)
- ec2_conn = boto.connect_ec2(aws_access_key_id=a_key,
- aws_secret_access_key=s_key,
- is_secure=is_secure,
- region=r,
- port=ec2_port,
- path=ec2_conn_path)
- return ec2_conn
-
-
-def get_or_create_cm_security_group(ec2_conn, sg_name='CloudManVPC'):
- """
- Create a security group with all authorizations required to run CloudMan.
- If the group already exists, check its rules and add the missing ones.
- Return the name of the created security group.
- """
- cm_sg = None
- # Check if this security group already exists. We can't use the built-in
- # filtering here, because VPC security groups can't be filtered by name.
- sg = ec2_conn.get_all_security_groups(filters={'group_name': sg_name})
- if sg:
- cm_sg = sg[0]
- else:
- # If it does not exist, create security group
- log.debug("Creating Security Group %s" % sg_name)
- cm_sg = ec2_conn.create_security_group(sg_name, 'A security group for CloudMan', vpc_id=get_or_create_cm_vpc(ec2_conn.access_key, ec2_conn.secret_key).id)
- # Add appropriate authorization rules
- # If these rules already exist, nothing will be changed in the SG
- ports = (('80', '80'), # Web UI
- ('20', '21'), # FTP
- ('22', '22'), # ssh
- ('30000', '30100'), # FTP transfer
- ('42284', '42284')) # CloudMan UI
- for port in ports:
- if not rule_exists(cm_sg.rules, from_port=port[0], to_port=port[1]):
- cm_sg.authorize(ip_protocol='tcp', from_port=port[0], to_port=port[1], cidr_ip='0.0.0.0/0')
- else:
- log.debug("Rule (%s:%s) already exists in the SG" % (port[0], port[1]))
- # Add rule that allows communication between instances in the same SG
- g_rule_exists = False # Flag to indicate if group rule already exists
- for rule in cm_sg.rules:
- for grant in rule.grants:#[g for g in rule.grants if g.name == cm_sg.name]:
- print grant.name
- if grant.name == cm_sg.name:
- g_rule_exists = True
- log.debug("Group rule already exists in the SG")
- if g_rule_exists:
- break
- #if g_rule_exists is False:
- # cm_sg.authorize(src_group=cm_sg)
- log.info("Done configuring '%s' security group" % cm_sg.name)
- return cm_sg
-
-
-
-def get_or_create_cm_vpc(a_key, s_key):
- vpc_conn = boto.vpc.VPCConnection(a_key, s_key)
- vpcs = vpc_conn.get_all_vpcs()
- cloudman_vpc = None
- for vpc in vpcs:
- if CLOUDMAN_TAG_KEY in vpc.tags:
- cloudman_vpc = vpc
- if not cloudman_vpc:
- #create a new one.
- cloudman_vpc = vpc_conn.create_vpc('10.0.0.0/16')
- cloudman_vpc.add_tag(CLOUDMAN_TAG_KEY, '')
- return cloudman_vpc
-
-
-def get_or_create_cm_subnet(a_key, s_key, availability_zone):
- log.debug("GETTING SUBNET in %s" % availability_zone)
- vpc_conn = boto.vpc.VPCConnection(a_key, s_key)
- subnets = vpc_conn.get_all_subnets()
- cloudman_subnet = None
- for subnet in subnets:
- log.debug("SN: %s, SNAZ:AZ: %s:%s:%s" % (subnet, subnet.availability_zone, availability_zone, subnet.availability_zone == availability_zone))
- if (not availability_zone or subnet.availability_zone == availability_zone) and CLOUDMAN_TAG_KEY in subnet.tags:
- cloudman_subnet = subnet
- if not cloudman_subnet:
- #create a new one.
- cloudman_subnet = vpc_conn.create_subnet(get_or_create_cm_vpc(a_key, s_key).id, '10.0.0.0/24', availability_zone)
- cloudman_subnet.add_tag(CLOUDMAN_TAG_KEY, '')
- return cloudman_subnet
-
-
-def _format_user_data(cluster_name, key_id, secret, password, share_string, bucket_default):
- user_provided_data = {'cluster_name': cluster_name,
- 'access_key': key_id,
- 'secret_key': secret}
- if password:
- user_provided_data['password'] = password
- if share_string:
- user_provided_data['share_string'] = share_string
- if bucket_default:
- user_provided_data['bucket_default'] = bucket_default
- return "\n".join(['%s: %s' % (key, value) for key, value in user_provided_data.iteritems() if key != 'kp_material'])
-
-
-def rule_exists(rules, from_port, to_port, ip_protocol='tcp', cidr_ip='0.0.0.0/0'):
- """ A convenience method to check if an authorization rule in a security
- group exists.
- """
- for rule in rules:
- if rule.ip_protocol == ip_protocol and rule.from_port == from_port and \
- rule.to_port == to_port and cidr_ip in [ip.cidr_ip for ip in rule.grants]:
- return True
- return False
-
-
-def create_key_pair(ec2_conn, key_name=DEFAULT_KEYPAIR):
- """ Create a key pair with the provided name.
- Return the name of the key or None if there was an error creating the key.
- """
- kp = None
- # Check if a key pair under the given name already exists. If it does not,
- # create it, else return.
- kps = ec2_conn.get_all_key_pairs()
- for akp in kps:
- if akp.name == key_name:
- log.debug("Key pair '%s' already exists; not creating it again." % key_name)
- return akp.name, None
- try:
- kp = ec2_conn.create_key_pair(key_name)
- except EC2ResponseError, e:
- log.error("Problem creating key pair '%s': %s" % (key_name, e))
- return None, None
- return kp.name, kp.material
-
-
-def _run_instance(ec2_conn, user_provided_data, instance_type, image_id=None,
- kernel_id=None, ramdisk_id=None, key_name=DEFAULT_KEYPAIR,
- placement=None, security_group_ids=None, subnet_id=None):
- """
- Start an instance. If instance start was OK, return the ResultSet object
- else return None.
- """
- rs = None
- try:
- rs = ec2_conn.run_instances(image_id=image_id,
- instance_type=instance_type,
- key_name=key_name,
- security_group_ids=security_group_ids,
- user_data=user_provided_data,
- kernel_id=kernel_id,
- subnet_id=subnet_id,
- ramdisk_id=ramdisk_id,
- placement=placement)
- except EC2ResponseError, e:
- log.error("Problem starting an instance: %s\n%s" % (e, e.body))
- if rs:
- try:
- log.info("Started an instance with ID %s" % rs.instances[0].id)
- except Exception, e:
- log.error("Problem with the started instance object: %s" % e)
- else:
- log.warning("Problem starting an instance?")
- return rs
diff -r 347a9169e3ec43a5719a4ca57d7de04ea50cd0e7 -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 templates/webapps/galaxy/cloud/index.mako
--- a/templates/webapps/galaxy/cloud/index.mako
+++ b/templates/webapps/galaxy/cloud/index.mako
@@ -65,7 +65,7 @@
clusterlist.append($('<option/>').val('New Cluster').text('New Cluster'));
if (_.size(result.clusters) > 0){
_.each(result.clusters, function(cluster, index){
- clusterlist.append($('<option/>').val(cluster.name).text(cluster.name));
+ clusterlist.append($('<option/>').val(cluster.cluster_name).text(cluster.cluster_name));
});
$('#existing_instance_wrapper').show();
}
@@ -95,13 +95,13 @@
type: 'POST',
dataType: 'json',
beforeSubmit: function(data, form){
- // Dig up zone info for selected cluster, set hidden input.
+ // Dig up placement info for selected cluster, set hidden input.
// This is not necessary to present to the user though the interface may prove useful.
var ei_val = _.find(data, function(f_obj){return f_obj.name === 'existing_instance'});
if( ei_val && (ei_val.value !== "New Cluster")){
- var cluster = _.find(cloudlaunch_clusters, function(cluster){return cluster.name === ei_val.value});
- var zdata = _.find(data, function(f_obj){return f_obj.name === 'zone'});
- zdata.value = cluster.zone;
+ var cluster = _.find(cloudlaunch_clusters, function(cluster){return cluster.cluster_name === ei_val.value});
+ var placement_field = _.find(data, function(f_obj){return f_obj.name === 'placement'});
+ placement_field.value = cluster.placement;
}else if($('#id_cluster_name').val() === ''){
// If we're not using an existing cluster, this must be set.
form.prepend('<div class="errormessage">You must specify a cluster name</div>');
@@ -188,7 +188,7 @@
<label for="id_existing_instance">Instances in your account</label><select name="existing_instance" id="id_existing_instance" style="min-width: 228px"></select>
- <input id='id_zone' type='hidden' name='zone' value=''/>
+ <input id='id_placement' type='hidden' name='placement' value=''/></div>
%endif
<div id='cluster_name_wrapper' class="form-row">
https://bitbucket.org/galaxy/galaxy-central/commits/557c0f2c6129/
Changeset: 557c0f2c6129
User: dannon
Date: 2014-04-21 23:10:48
Summary: Merge.
Affected #: 372 files
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -6,3 +6,4 @@
1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12
26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04
5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10
+9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -51,7 +51,7 @@
// append views
this.$el.append(this.viewer_view.$el);
this.$el.append(this.editor_view.$el);
-
+
// pick start screen
if (!this.storage.load()) {
// show editor
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
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n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"chartskit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:a,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the Charts-Kit. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh")},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._create_svg();var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_create_svg:function(){this.svg&&this.svg.remove(),this.$el.append($(this._template_svg())),this.svg_el=this.$el.find("svg"),this.svg=d3.select(this.svg_el[0])},_draw:function(e){var t=this;this._create_svg(),e.state("wait","Please wait...");var n=e.deferred.register(),r=e.get("type"),i=this.app.types.get(r);if(!i.execute||i.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var s=new r(t.app,{svg:t.svg});i.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){s.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):s.draw(n,e,t._defaultRequestDictionary(e)):s.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={groups:[]};t.execute?n.id=e.get("dataset_id_job"):n.id=e.get("dataset_id");var r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n},_template:function(){return'<div style="height: 100%; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_svg:function(){return'<svg style="height: calc(100% - 80px)"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Customize",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("wait","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var 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'+e.title+"</div>"}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a 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onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:i,Icon:s,ButtonIcon:o,Input:h,Anchor:u,Message:a,Searchbox:f,Title:l,Text:r,Select:t,ButtonMenu:c}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({canvas:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._create_canvas("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_create_canvas:function(e,t){t=t||1;for(var n in this.canvas)this.canvas[n].remove(),this.canvas.slice(n,0);for(var n=0;n<t;n++){var r=$(this._template_canvas(e,parseInt(100/t)));this.$el.append(r),e=="svg"?this.canvas[n]=d3.select(r[0]):this.canvas[n]=r}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._create_canvas(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var i=new r(t.app,{canvas:t.canvas});t.chart_settings.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e)):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div style="height: inherit; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_canvas:function(e,t){return"<"+e+' class="canvas" style="float: left; display: block; width:'+t+'%; height: 100%;"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onchange:function(e){u.chart.settings.clear(),u.chart.set({type:e}),u.chart.set("modified",!0)},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"}),this.table.addHeader("No."),this.table.addHeader("Type"),this.table.addHeader("Library"),this.table.addHeader("Processing*"),this.table.appendHeader();var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),this.table.add(h.title),this.table.add(h.library,"10%"),h.execute?this.table.add((new n.Icon({icon:"fa-check"})).$el,"10%","center"):this.table.add(""),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),p.append((new n.Text({title:"*Certain chart types pre-process data before rendering the visualization. The pre-processing is done using the chartskit available in the Toolshed.",cls:"toolParamHelp"})).$el),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","nvd3_bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bardiagram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/nvd3_linewithfocus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/nvd3_piechart/config",[],function(){return{title:"Pie chart",library:"nvd3.js",tag:"svg",use_panels:!0,columns:{label:{title:"Labels",is_label:!0},y:{title:"Values"}},settings:{show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_scatterplot/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",library:"highcharts.js",element:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/types",["plugin/charts/nvd3_bardiagram/config","plugin/charts/nvd3_histogram/config","plugin/charts/nvd3_horizontal/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_linewithfocus/config","plugin/charts/nvd3_piechart/config","plugin/charts/nvd3_scatterplot/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/highcharts_boxplot/config"],function(e,t,n,r,i,s,o,u,a){return Backbone.Model.extend({defaults:{nvd3_bardiagram:e,nvd3_horizontal:n,nvd3_histogram:t,nvd3_line:r,nvd3_linewithfocus:i,nvd3_piechart:s,nvd3_scatterplot:o,nvd3_stackedarea:u,highcharts_boxplot:a}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/_nvd3/config.js
--- a/config/plugins/visualizations/charts/static/charts/_nvd3/config.js
+++ /dev/null
@@ -1,218 +0,0 @@
-define([], function() {
-
-return {
- title : '',
- columns : {
- y : {
- title : 'Values for y-axis'
- }
- },
- settings : {
- separator_label : {
- title : 'X axis',
- type : 'separator'
- },
- x_axis_label : {
- title : 'Axis label',
- info : 'Provide a label for the axis.',
- type : 'text',
- init : 'X-axis',
- placeholder : 'Axis label'
- },
- x_axis_type : {
- title : 'Axis value type',
- info : 'Select the value type of the axis.',
- type : 'select',
- init : 'auto',
- data : [
- {
- label : '-- Do not show values --',
- value : 'hide',
- hide : 'x_axis_tick'
- },
- {
- label : 'Auto',
- value : 'auto',
- hide : 'x_axis_tick'
- },
- {
- label : 'Float',
- value : 'f',
- show : 'x_axis_tick'
- },
- {
- label : 'Exponent',
- value : 'e',
- show : 'x_axis_tick'
- },
- {
- label : 'Integer',
- value : 'd',
- hide : 'x_axis_tick'
- },
- {
- label : 'Percentage',
- value : 'p',
- show : 'x_axis_tick'
- },
- {
- label : 'Rounded',
- value : 'r',
- show : 'x_axis_tick'
- },
- {
- label : 'SI-prefix',
- value : 's',
- show : 'x_axis_tick'
- }
- ]
- },
- x_axis_tick : {
- title : 'Axis tick format',
- info : 'Select the tick format for the axis.',
- type : 'select',
- init : '.1',
- data : [
- {
- label : '0.00001',
- value : '.5'
- },
- {
- label : '0.0001',
- value : '.4'
- },
- {
- label : '0.001',
- value : '.3'
- },
- {
- label : '0.01',
- value : '.2'
- },
- {
- label : '0.1',
- value : '.1'
- },
- {
- label : '1',
- value : '1'
- }
- ]
-
- },
- separator_tick : {
- title : 'Y axis',
- type : 'separator'
- },
- y_axis_label : {
- title : 'Axis label',
- info : 'Provide a label for the axis.',
- type : 'text',
- init : 'Y-axis',
- placeholder : 'Axis label'
- },
- y_axis_type : {
- title : 'Axis value type',
- info : 'Select the value type of the axis.',
- type : 'select',
- init : 'auto',
- data : [
- {
- label : '-- Do not show values --',
- value : 'hide',
- hide : 'y_axis_tick'
- },
- {
- label : 'Auto',
- value : 'auto',
- hide : 'y_axis_tick'
- },
- {
- label : 'Float',
- value : 'f',
- show : 'y_axis_tick'
- },
- {
- label : 'Exponent',
- value : 'e',
- show : 'y_axis_tick'
- },
- {
- label : 'Integer',
- value : 'd',
- hide : 'y_axis_tick'
- },
- {
- label : 'Percentage',
- value : 'p',
- show : 'y_axis_tick'
- },
- {
- label : 'Rounded',
- value : 'r',
- show : 'y_axis_tick'
- },
- {
- label : 'SI-prefix',
- value : 's',
- show : 'y_axis_tick'
- }
- ]
- },
- y_axis_tick : {
- title : 'Axis tick format',
- info : 'Select the tick format for the axis.',
- type : 'select',
- init : '.1',
- data : [
- {
- label : '0.00001',
- value : '.5'
- },
- {
- label : '0.0001',
- value : '.4'
- },
- {
- label : '0.001',
- value : '.3'
- },
- {
- label : '0.01',
- value : '.2'
- },
- {
- label : '0.1',
- value : '.1'
- },
- {
- label : '1',
- value : '1'
- }
- ]
-
- },
- separator_legend : {
- title : 'Others',
- type : 'separator'
- },
- show_legend : {
- title : 'Show legend',
- info : 'Would you like to add a legend?',
- type : 'select',
- init : 'true',
- data : [
- {
- label : 'Yes',
- value : 'true'
- },
- {
- label : 'No',
- value : 'false'
- }
- ]
- },
- }
-};
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
--- a/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
+++ /dev/null
@@ -1,80 +0,0 @@
-// dependencies
-define([], function() {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, nvd3_model, chart, request_dictionary, callback)
- {
- // request data
- var self = this;
- this.app.datasets.request(request_dictionary, function(data) {
- nv.addGraph(function() {
- // x axis
- self._axis(nvd3_model.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick'));
-
- // x axis label
- nvd3_model.xAxis.axisLabel(chart.settings.get('x_axis_label'));
-
- // y axis
- self._axis(nvd3_model.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick'));
-
- // y axis label
- nvd3_model.yAxis.axisLabel(chart.settings.get('y_axis_label'))
- .axisLabelDistance(30);
-
- // controls
- if (chart.groups.length == 1) {
- nvd3_model.options({ showControls: false });
- }
-
- // legend
- var legend_visible = true;
- if (chart.settings.get('show_legend') == 'false') {
- legend_visible = false;
- }
- nvd3_model.showLegend(legend_visible);
-
- // custom callback
- if (callback) {
- callback(nvd3_model);
- }
-
- // parse data to svg
- self.options.svg.datum(data)
- .call(nvd3_model);
-
- // refresh on window resize
- nv.utils.windowResize(nvd3_model.update);
-
- // set chart state
- chart.state('ok', 'Chart has been drawn.');
-
- // unregister process
- chart.deferred.done(process_id);
- });
- });
- },
-
- // make axis
- _axis: function(axis, type, tick) {
- switch (type) {
- case 'hide':
- axis.tickFormat(function() { return '' });
- break;
- case 'auto':
- break;
- default:
- axis.tickFormat(d3.format(tick + type));
- }
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js
--- a/config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/bardiagram/config.js
--- a/config/plugins/visualizations/charts/static/charts/bardiagram/config.js
+++ /dev/null
@@ -1,7 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Bar diagram',
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js
@@ -0,0 +1,39 @@
+define([], function() {
+
+return {
+ title : 'Box plot',
+ library : 'highcharts.js',
+ element : 'div',
+ execute : 'boxplot',
+ columns : {
+ y : {
+ title : 'Observations'
+ }
+ },
+ settings : {
+ separator_label : {
+ title : 'X axis',
+ type : 'separator'
+ },
+ x_axis_label : {
+ title : 'Axis label',
+ info : 'Provide a label for the axis.',
+ type : 'text',
+ init : 'X-axis',
+ placeholder : 'Axis label'
+ },
+ separator_tick : {
+ title : 'Y axis',
+ type : 'separator'
+ },
+ y_axis_label : {
+ title : 'Axis label',
+ info : 'Provide a label for the axis.',
+ type : 'text',
+ init : 'Y-axis',
+ placeholder : 'Axis label'
+ }
+ }
+};
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js
@@ -0,0 +1,122 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.View.extend(
+{
+ // highcharts configuration
+ hc_config : {
+ chart: {
+ type: 'boxplot'
+ },
+
+ title: {
+ text: ''
+ },
+
+ legend: {
+ enabled: false
+ },
+
+ credits: {
+ enabled: false
+ },
+
+ plotOptions: {
+ series: {
+ animation: false
+ }
+ },
+
+ xAxis: {
+ categories: [],
+ title: {
+ text: ''
+ }
+ },
+
+ yAxis: {
+ title: {
+ text: ''
+ }
+ },
+
+ series: [{
+ name: 'Details:',
+ data: [],
+ tooltip: {
+ headerFormat: '<em>{point.key}</em><br/>'
+ }
+ }]
+ },
+
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // configure request
+ var index = 0;
+ for (var i in request_dictionary.groups) {
+ var group = request_dictionary.groups[i];
+ group.columns = null;
+ group.columns = {
+ x: {
+ index: index++
+ }
+ }
+ }
+
+ // set axis labels
+ this.hc_config.xAxis.title.text = chart.settings.get('x_axis_label');
+ this.hc_config.yAxis.title.text = chart.settings.get('y_axis_label');
+
+ // request data
+ var self = this;
+ this.app.datasets.request(request_dictionary, function() {
+
+ // reset data/categories
+ var data = [];
+ var categories = [];
+
+ // loop through data groups
+ for (var key in request_dictionary.groups) {
+ // get group
+ var group = request_dictionary.groups[key];
+
+ // add category
+ categories.push(group.key);
+
+ // format chart data
+ var point = [];
+ for (var key in group.values) {
+ point.push(group.values[key].x);
+ }
+
+ // add to data
+ data.push (point);
+ }
+
+ // categories
+ self.hc_config.xAxis.categories = categories;
+
+ // update data
+ self.hc_config.series[0].data = data;
+
+ // draw plot
+ self.options.canvas[0].highcharts(self.hc_config);
+
+ // set chart state
+ chart.state('ok', 'Box plot drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/histogram/config.js
--- a/config/plugins/visualizations/charts/static/charts/histogram/config.js
+++ /dev/null
@@ -1,21 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Histogram',
- execute : true,
- columns : {
- y : {
- title : 'Observations'
- }
- },
- settings : {
- x_axis_label : {
- init : 'Breaks'
- },
- y_axis_label : {
- init : 'Density'
- }
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/histogram/histogram.js
--- a/config/plugins/visualizations/charts/static/charts/histogram/histogram.js
+++ /dev/null
@@ -1,31 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- // configure request
- var index = 0;
- for (var i in request_dictionary.groups) {
- var group = request_dictionary.groups[i];
- group.columns = {
- x: index++,
- y: index++
- }
- }
-
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/horizontal/config.js
--- a/config/plugins/visualizations/charts/static/charts/horizontal/config.js
+++ /dev/null
@@ -1,12 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Bar diagram (horizontal)',
- settings : {
- x_axis_type : {
- init : 'hide'
- }
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js
--- a/config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/line/config.js
--- a/config/plugins/visualizations/charts/static/charts/line/config.js
+++ /dev/null
@@ -1,7 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Line chart',
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/line/line.js
--- a/config/plugins/visualizations/charts/static/charts/line/line.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/linewithfocus/config.js
--- a/config/plugins/visualizations/charts/static/charts/linewithfocus/config.js
+++ /dev/null
@@ -1,7 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Line with focus',
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js
--- a/config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/config.js
@@ -0,0 +1,220 @@
+define([], function() {
+
+return {
+ title : '',
+ library : 'nvd3.js',
+ tag : 'svg',
+ columns : {
+ y : {
+ title : 'Values for y-axis'
+ }
+ },
+ settings : {
+ separator_label : {
+ title : 'X axis',
+ type : 'separator'
+ },
+ x_axis_label : {
+ title : 'Axis label',
+ info : 'Provide a label for the axis.',
+ type : 'text',
+ init : 'X-axis',
+ placeholder : 'Axis label'
+ },
+ x_axis_type : {
+ title : 'Axis value type',
+ info : 'Select the value type of the axis.',
+ type : 'select',
+ init : 'auto',
+ data : [
+ {
+ label : '-- Do not show values --',
+ value : 'hide',
+ hide : 'x_axis_tick'
+ },
+ {
+ label : 'Auto',
+ value : 'auto',
+ hide : 'x_axis_tick'
+ },
+ {
+ label : 'Float',
+ value : 'f',
+ show : 'x_axis_tick'
+ },
+ {
+ label : 'Exponent',
+ value : 'e',
+ show : 'x_axis_tick'
+ },
+ {
+ label : 'Integer',
+ value : 'd',
+ hide : 'x_axis_tick'
+ },
+ {
+ label : 'Percentage',
+ value : 'p',
+ show : 'x_axis_tick'
+ },
+ {
+ label : 'Rounded',
+ value : 'r',
+ show : 'x_axis_tick'
+ },
+ {
+ label : 'SI-prefix',
+ value : 's',
+ show : 'x_axis_tick'
+ }
+ ]
+ },
+ x_axis_tick : {
+ title : 'Axis tick format',
+ info : 'Select the tick format for the axis.',
+ type : 'select',
+ init : '.1',
+ data : [
+ {
+ label : '0.00001',
+ value : '.5'
+ },
+ {
+ label : '0.0001',
+ value : '.4'
+ },
+ {
+ label : '0.001',
+ value : '.3'
+ },
+ {
+ label : '0.01',
+ value : '.2'
+ },
+ {
+ label : '0.1',
+ value : '.1'
+ },
+ {
+ label : '1',
+ value : '1'
+ }
+ ]
+
+ },
+ separator_tick : {
+ title : 'Y axis',
+ type : 'separator'
+ },
+ y_axis_label : {
+ title : 'Axis label',
+ info : 'Provide a label for the axis.',
+ type : 'text',
+ init : 'Y-axis',
+ placeholder : 'Axis label'
+ },
+ y_axis_type : {
+ title : 'Axis value type',
+ info : 'Select the value type of the axis.',
+ type : 'select',
+ init : 'auto',
+ data : [
+ {
+ label : '-- Do not show values --',
+ value : 'hide',
+ hide : 'y_axis_tick'
+ },
+ {
+ label : 'Auto',
+ value : 'auto',
+ hide : 'y_axis_tick'
+ },
+ {
+ label : 'Float',
+ value : 'f',
+ show : 'y_axis_tick'
+ },
+ {
+ label : 'Exponent',
+ value : 'e',
+ show : 'y_axis_tick'
+ },
+ {
+ label : 'Integer',
+ value : 'd',
+ hide : 'y_axis_tick'
+ },
+ {
+ label : 'Percentage',
+ value : 'p',
+ show : 'y_axis_tick'
+ },
+ {
+ label : 'Rounded',
+ value : 'r',
+ show : 'y_axis_tick'
+ },
+ {
+ label : 'SI-prefix',
+ value : 's',
+ show : 'y_axis_tick'
+ }
+ ]
+ },
+ y_axis_tick : {
+ title : 'Axis tick format',
+ info : 'Select the tick format for the axis.',
+ type : 'select',
+ init : '.1',
+ data : [
+ {
+ label : '0.00001',
+ value : '.5'
+ },
+ {
+ label : '0.0001',
+ value : '.4'
+ },
+ {
+ label : '0.001',
+ value : '.3'
+ },
+ {
+ label : '0.01',
+ value : '.2'
+ },
+ {
+ label : '0.1',
+ value : '.1'
+ },
+ {
+ label : '1',
+ value : '1'
+ }
+ ]
+
+ },
+ separator_legend : {
+ title : 'Others',
+ type : 'separator'
+ },
+ show_legend : {
+ title : 'Show legend',
+ info : 'Would you like to add a legend?',
+ type : 'select',
+ init : 'true',
+ data : [
+ {
+ label : 'Yes',
+ value : 'true'
+ },
+ {
+ label : 'No',
+ value : 'false'
+ }
+ ]
+ }
+ }
+};
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js
@@ -0,0 +1,80 @@
+// dependencies
+define([], function() {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, nvd3_model, chart, request_dictionary, callback)
+ {
+ // request data
+ var self = this;
+ this.app.datasets.request(request_dictionary, function() {
+ nv.addGraph(function() {
+ // x axis
+ self._axis(nvd3_model.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick'));
+
+ // x axis label
+ nvd3_model.xAxis.axisLabel(chart.settings.get('x_axis_label'));
+
+ // y axis
+ self._axis(nvd3_model.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick'));
+
+ // y axis label
+ nvd3_model.yAxis.axisLabel(chart.settings.get('y_axis_label'))
+ .axisLabelDistance(30);
+
+ // controls
+ if (chart.groups.length == 1) {
+ nvd3_model.options({ showControls: false });
+ }
+
+ // legend
+ var legend_visible = true;
+ if (chart.settings.get('show_legend') == 'false') {
+ legend_visible = false;
+ }
+ nvd3_model.showLegend(legend_visible);
+
+ // custom callback
+ if (callback) {
+ callback(nvd3_model);
+ }
+
+ // parse data to canvas
+ self.options.canvas[0].datum(request_dictionary.groups)
+ .call(nvd3_model);
+
+ // refresh on window resize
+ nv.utils.windowResize(nvd3_model.update);
+
+ // set chart state
+ chart.state('ok', 'Chart has been drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ });
+ });
+ },
+
+ // make axis
+ _axis: function(axis, type, tick) {
+ switch (type) {
+ case 'hide':
+ axis.tickFormat(function() { return '' });
+ break;
+ case 'auto':
+ break;
+ default:
+ axis.tickFormat(d3.format(tick + type));
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Bar diagram',
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/nvd3_bardiagram.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/nvd3_bardiagram.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_histogram/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram/config.js
@@ -0,0 +1,27 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Histogram',
+ execute : 'histogram',
+ columns : {
+ y : {
+ title : 'Observations'
+ }
+ },
+ settings : {
+ x_axis_label : {
+ init : 'Breaks'
+ },
+ y_axis_label : {
+ init : 'Density'
+ },
+ y_axis_type : {
+ init : 'f'
+ },
+ y_axis_tick : {
+ init : '.2'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_histogram/nvd3_histogram.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram/nvd3_histogram.js
@@ -0,0 +1,39 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // configure request
+ var index = 1;
+ for (var i in request_dictionary.groups) {
+ var group = request_dictionary.groups[i];
+ group.columns = {
+ x: {
+ index: 0
+ },
+ y: {
+ index: index++
+ },
+ }
+ }
+
+ // link this
+ var self = this;
+
+ // load nvd3
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_horizontal/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_horizontal/config.js
@@ -0,0 +1,12 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Bar diagram (horizontal)',
+ settings : {
+ x_axis_type : {
+ init : 'hide'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_horizontal/nvd3_horizontal.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_horizontal/nvd3_horizontal.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_line/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_line/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Line chart',
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_line/nvd3_line.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_line/nvd3_line.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Line with focus',
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/nvd3_linewithfocus.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/nvd3_linewithfocus.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary);
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js
@@ -0,0 +1,114 @@
+define([], function() {
+
+return {
+ title : 'Pie chart',
+ library : 'nvd3.js',
+ tag : 'svg',
+ use_panels : true,
+ columns : {
+ label : {
+ title : 'Labels',
+ is_label : true
+ },
+ y : {
+ title : 'Values'
+ }
+ },
+
+ settings : {
+ show_legend : {
+ title : 'Show legend',
+ info : 'Would you like to add a legend?',
+ type : 'select',
+ init : 'false',
+ data : [
+ {
+ label : 'Yes',
+ value : 'true'
+ },
+ {
+ label : 'No',
+ value : 'false'
+ }
+ ]
+ },
+
+ donut_ratio : {
+ title : 'Donut ratio',
+ info : 'Determine how large the donut hole will be.',
+ type : 'select',
+ init : '0.5',
+ data : [
+ {
+ label : '50%',
+ value : '0.5'
+ },
+ {
+ label : '25%',
+ value : '0.25'
+ },
+ {
+ label : '10%',
+ value : '0.10'
+ },
+ {
+ label : '0%',
+ value : '0'
+ }
+ ]
+ },
+
+ label_separator : {
+ type : 'separator',
+ title : 'Label settings'
+ },
+
+ label_type : {
+ title : 'Donut label',
+ info : 'What would you like to show for each slice?',
+ type : 'select',
+ init : 'percent',
+ data : [
+ {
+ label : '-- Nothing --',
+ value : 'hide',
+ hide : 'label_outside'
+ },
+ {
+ label : 'Label column',
+ value : 'key',
+ show : 'label_outside'
+ },
+ {
+ label : 'Value column',
+ value : 'value',
+ show : 'label_outside'
+ },
+ {
+ label : 'Percentage',
+ value : 'percent',
+ show : 'label_outside'
+ }
+ ],
+ },
+
+ label_outside : {
+ title : 'Show outside',
+ info : 'Would you like to show labels outside the donut?',
+ type : 'select',
+ init : 'false',
+ data : [
+ {
+ label : 'Yes',
+ value : 'true'
+ },
+ {
+ label : 'No',
+ value : 'false'
+ }
+ ]
+ }
+ }
+};
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js
@@ -0,0 +1,115 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // request data
+ var self = this;
+ this.app.datasets.request(request_dictionary, function() {
+
+ // loop through data groups
+ for (var group_index in request_dictionary.groups) {
+ // get group
+ var group = request_dictionary.groups[group_index];
+
+ // draw group
+ self._draw_group(chart, group, self.options.canvas[group_index]);
+ }
+
+ // set chart state
+ chart.state('ok', 'Pie chart has been drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ });
+ },
+
+ // draw group
+ _draw_group: function(chart, group, canvas) {
+
+ // add title
+ var title = canvas.append('text');
+
+ // configure title attributes
+ this._fix_title(chart, canvas, title, group.key);
+
+ // format chart data
+ var pie_data = [];
+ for (var key in group.values) {
+ var value = group.values[key];
+ pie_data.push ({
+ y : value.y,
+ x : value.label
+ });
+ }
+
+ // add graph to screen
+ var self = this;
+ nv.addGraph(function() {
+ // legend
+ var legend_visible = true;
+ if (chart.settings.get('show_legend') == 'false') {
+ legend_visible = false;
+ }
+
+ // legend
+ var label_outside = true;
+ if (chart.settings.get('label_outside') == 'false') {
+ label_outside = false;
+ }
+
+ // label type
+ var label_type = chart.settings.get('label_type');
+
+ // ratio
+ var donut_ratio = parseFloat(chart.settings.get('donut_ratio'))
+
+ // create chart model
+ var chart_3d = nv.models.pieChart()
+ .donut(true)
+ .labelThreshold(.05)
+ .showLegend(legend_visible)
+ .labelType(label_type)
+ .donutRatio(donut_ratio)
+ .donutLabelsOutside(label_outside);
+
+ // add data to canvas
+ canvas.datum(pie_data)
+ .call(chart_3d);
+
+ // add resize trigger
+ nv.utils.windowResize(function() {
+ // update chart
+ chart_3d.update();
+
+ // fix title
+ self._fix_title(chart, canvas, title, group.key);
+ });
+ });
+ },
+
+ // fix title
+ _fix_title: function(chart, canvas, title_element, title_text) {
+ // update title
+ var width = parseInt(canvas.style('width'));
+ var height = parseInt(canvas.style('height'));
+
+ // add title
+ title_element.attr('x', width / 2)
+ .attr('y', height - 10)
+ .attr('text-anchor', 'middle')
+ .text(title_text);
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/config.js
@@ -0,0 +1,12 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Scatter plot',
+ columns : {
+ x : {
+ title : 'Values for x-axis'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/nvd3_scatterplot.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/nvd3_scatterplot.js
@@ -0,0 +1,25 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.scatterChart(), chart, request_dictionary, function(nvd3_model) {
+ nvd3_model.showDistX(true)
+ .showDistY(true)
+ .color(d3.scale.category10().range());
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+ title : 'Stacked area'
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/nvd3_stackedarea.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/nvd3_stackedarea.js
@@ -0,0 +1,26 @@
+// dependencies
+define(['plugin/charts/nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ var nvd3 = new NVD3(this.app, this.options);
+ nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) {
+ // make plot
+ nvd3_model.x(function(d) { return d.x })
+ .y(function(d) { return d.y })
+ .clipEdge(true);
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/piechart/config.js
--- a/config/plugins/visualizations/charts/static/charts/piechart/config.js
+++ /dev/null
@@ -1,7 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Pie chart',
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/piechart/piechart.js
--- a/config/plugins/visualizations/charts/static/charts/piechart/piechart.js
+++ /dev/null
@@ -1,57 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- // request data
- var self = this;
- this.app.datasets.request(request_dictionary, function(data) {
-
- // loop through data groups
- for (var key in request_dictionary.groups) {
- // get group
- var group = request_dictionary.groups[key];
-
- // format chart data
- var pie_data = [];
- for (var key in group.values) {
- var value = group.values[key];
- pie_data.push ({
- key : value.x,
- y : value.y
- });
- }
-
- // add graph to screen
- nv.addGraph(function() {
- self.chart_3d = nv.models.pieChart()
- .donut(true)
- .showLegend(false);
-
- self.options.svg.datum(pie_data)
- .call(self.chart_3d);
-
- nv.utils.windowResize(self.chart_3d.update);
-
- // set chart state
- chart.state('ok', 'Pie chart drawn.');
-
- // unregister process
- chart.deferred.done(process_id);
- });
- }
- });
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/scatterplot/config.js
--- a/config/plugins/visualizations/charts/static/charts/scatterplot/config.js
+++ /dev/null
@@ -1,12 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Scatter plot',
- columns : {
- x : {
- title : 'Values for x-axis'
- }
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/scatterplot/scatterplot.js
--- a/config/plugins/visualizations/charts/static/charts/scatterplot/scatterplot.js
+++ /dev/null
@@ -1,25 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.scatterChart(), chart, request_dictionary, function(nvd3_model) {
- nvd3_model.showDistX(true)
- .showDistY(true)
- .color(d3.scale.category10().range());
- });
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/stackedarea/config.js
--- a/config/plugins/visualizations/charts/static/charts/stackedarea/config.js
+++ /dev/null
@@ -1,7 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Stacked area'
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/stackedarea/stackedarea.js
--- a/config/plugins/visualizations/charts/static/charts/stackedarea/stackedarea.js
+++ /dev/null
@@ -1,26 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) {
- // make plot
- nvd3_model.x(function(d) { return d.x })
- .y(function(d) { return d.y })
- .clipEdge(true);
- });
- }
-});
-
-});
\ No newline at end of file
diff -r 19e8344a0497c1dc8009b93bbef3ce3ca4e8ece5 -r 557c0f2c6129026d8a6738292a4ae26e681e1391 config/plugins/visualizations/charts/static/charts/types.js
--- a/config/plugins/visualizations/charts/static/charts/types.js
+++ b/config/plugins/visualizations/charts/static/charts/types.js
@@ -1,22 +1,22 @@
// dependencies
-define(['plugin/charts/bardiagram/config',
- //'plugin/charts/boxplot/config',
- 'plugin/charts/histogram/config',
- 'plugin/charts/horizontal/config',
- 'plugin/charts/line/config',
- 'plugin/charts/linewithfocus/config',
- 'plugin/charts/piechart/config',
- 'plugin/charts/scatterplot/config',
- 'plugin/charts/stackedarea/config',
- ], function(bardiagram,
- //boxplot,
- histogram,
- horizontal,
- line,
- linewithfocus,
- piechart,
- scatterplot,
- stackedarea
+define(['plugin/charts/nvd3_bardiagram/config',
+ 'plugin/charts/nvd3_histogram/config',
+ 'plugin/charts/nvd3_horizontal/config',
+ 'plugin/charts/nvd3_line/config',
+ 'plugin/charts/nvd3_linewithfocus/config',
+ 'plugin/charts/nvd3_piechart/config',
+ 'plugin/charts/nvd3_scatterplot/config',
+ 'plugin/charts/nvd3_stackedarea/config',
+ 'plugin/charts/highcharts_boxplot/config',
+ ], function(nvd3_bardiagram,
+ nvd3_histogram,
+ nvd3_horizontal,
+ nvd3_line,
+ nvd3_linewithfocus,
+ nvd3_piechart,
+ nvd3_scatterplot,
+ nvd3_stackedarea,
+ highcharts_boxplot
) {
// widget
@@ -24,15 +24,15 @@
{
// types
defaults: {
- 'bardiagram' : bardiagram,
- //'boxplot' : boxplot,
- 'horizontal' : horizontal,
- 'histogram' : histogram,
- 'line' : line,
- 'linewithfocus' : linewithfocus,
- 'piechart' : piechart,
- 'scatterplot' : scatterplot,
- 'stackedarea' : stackedarea
+ 'nvd3_bardiagram' : nvd3_bardiagram,
+ 'nvd3_horizontal' : nvd3_horizontal,
+ 'nvd3_histogram' : nvd3_histogram,
+ 'nvd3_line' : nvd3_line,
+ 'nvd3_linewithfocus' : nvd3_linewithfocus,
+ 'nvd3_piechart' : nvd3_piechart,
+ 'nvd3_scatterplot' : nvd3_scatterplot,
+ 'nvd3_stackedarea' : nvd3_stackedarea,
+ 'highcharts_boxplot' : highcharts_boxplot
}
});
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: davebgx: Fix functional tests for library features.
by commits-noreply＠bitbucket.org 21 Apr '14
by commits-noreply＠bitbucket.org 21 Apr '14
21 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/46f414686496/
Changeset: 46f414686496
User: davebgx
Date: 2014-04-21 22:51:05
Summary: Fix functional tests for library features.
Affected #: 2 files
diff -r 646c971309f3fce14d5e95a709e9ca881e0ca0f0 -r 46f414686496939dab3337ec4301e41973b1af56 templates/webapps/galaxy/library/common/move_library_item.mako
--- a/templates/webapps/galaxy/library/common/move_library_item.mako
+++ b/templates/webapps/galaxy/library/common/move_library_item.mako
@@ -67,7 +67,7 @@
<div class="toolFormBody">
%if target_library:
<div class="form-row">
- %if len( target_folder_id_select_field.options ) > 1:
+ %if len( target_folder_id_select_field.options ) >= 1:
${target_folder_id_select_field.get_html()}
%else:
%if source_library and source_library.id == target_library.id:
diff -r 646c971309f3fce14d5e95a709e9ca881e0ca0f0 -r 46f414686496939dab3337ec4301e41973b1af56 test/base/twilltestcase.py
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -194,6 +194,12 @@
file_dir = self.file_dir
return os.path.abspath( os.path.join( file_dir, filename ) )
+ def get_form_controls( self, form ):
+ formcontrols = []
+ for i, control in enumerate( form.controls ):
+ formcontrols.append( "control %d: %s" % ( i, str( control ) ) )
+ return formcontrols
+
def save_log( *path ):
"""Saves the log to a file"""
filename = os.path.join( *path )
@@ -1234,11 +1240,9 @@
# To help with debugging a tool, print out the form controls when the test fails
print "form '%s' contains the following controls ( note the values )" % f.name
controls = {}
- formcontrols = []
+ formcontrols = self.get_form_controls( f )
hc_prefix = '<HiddenControl('
for i, control in enumerate( f.controls ):
- formcontrols.append( "control %d: %s" % ( i, str( control ) ) )
- for i, control in enumerate( f.controls ):
if not hc_prefix in str( control ):
try:
#check if a repeat element needs to be added
@@ -1353,16 +1357,18 @@
pass
tc.submit( button )
- def refresh_form( self, control_name, value, form_no=0, form_id=None, **kwd ):
+ def refresh_form( self, control_name, value, form_no=0, form_id=None, form_name=None, **kwd ):
"""Handles Galaxy's refresh_on_change for forms without ultimately submitting the form"""
# control_name is the name of the form field that requires refresh_on_change, and value is
# the value to which that field is being set.
for i, f in enumerate( self.showforms() ):
- if i == form_no or ( form_id is not None and f.id == form_id ):
+ if i == form_no or ( form_id is not None and f.id == form_id ) or ( form_name is not None and f.name == form_name ):
break
+ formcontrols = self.get_form_controls( f )
try:
control = f.find_control( name=control_name )
except:
+ log.debug( '\n'.join( formcontrols ) )
# This assumes we always want the first control of the given name, which may not be ideal...
control = f.find_control( name=control_name, nr=0 )
# Check for refresh_on_change attribute, submit a change if required
@@ -2534,13 +2540,22 @@
errmsg += 'Unpacked archive remains in: %s\n' % tmpd
raise AssertionError( errmsg )
shutil.rmtree( tmpd )
+
def move_library_item( self, cntrller, item_type, item_id, source_library_id, make_target_current,
- target_library_id='', target_folder_id='', strings_displayed=[], strings_displayed_after_submit=[] ):
+ target_library_id=None, target_folder_id=None, strings_displayed=[], strings_displayed_after_submit=[] ):
self.home()
- self.visit_url( "%s/library_common/move_library_item?cntrller=%s&item_type=%s&item_id=%s&source_library_id=%s&make_target_current=%s" \
- % ( self.url, cntrller, item_type, item_id, source_library_id, make_target_current ) )
+ params = dict( cntrller=cntrller,
+ item_type=item_type,
+ item_id=item_id,
+ source_library_id=source_library_id,
+ make_target_current=make_target_current )
+ if target_library_id is not None:
+ params[ 'target_library_id' ] = target_library_id
+ if target_folder_id is not None:
+ params[ 'target_folder_id' ] = target_folder_id
+ self.visit_url( "%s/library_common/move_library_item?%s" % ( self.url, urllib.urlencode( params ) ) )
if target_library_id:
- self.refresh_form( 'target_library_id', target_library_id )
+ self.refresh_form( 'target_library_id', target_library_id, form_name='move_library_item' )
if target_folder_id:
tc.fv( '1', 'target_folder_id', target_folder_id )
for check_str in strings_displayed:
@@ -2549,6 +2564,7 @@
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
self.home()
+
def delete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ):
"""Mark a library item as deleted"""
self.home()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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