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November 2014

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commit/galaxy-central: martenson: initial commit of google analytics tracking for toolshed
by commits-noreply＠bitbucket.org 04 Nov '14

04 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/29a536155bf4/ Changeset: 29a536155bf4 User: martenson Date: 2014-11-04 15:31:15+00:00 Summary: initial commit of google analytics tracking for toolshed Affected #: 3 files diff -r d53d0150e936944c6a9e10dad1533a9645d37c48 -r 29a536155bf46e3c3dfa4f17760fda17f1e1835d config/tool_shed.ini.sample --- a/config/tool_shed.ini.sample +++ b/config/tool_shed.ini.sample @@ -46,6 +46,12 @@ session_key = galaxysessions session_secret = changethisinproduction +# -- Analytics + +# You can enter tracking code here to track visitor's behavior +# through your Google Analytics account. Example: UA-XXXXXXXX-Y +#ga_code = None + # -- Users and Security # Galaxy encodes various internal values when these values will be output in diff -r d53d0150e936944c6a9e10dad1533a9645d37c48 -r 29a536155bf46e3c3dfa4f17760fda17f1e1835d lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -40,6 +40,8 @@ self.database_connection = kwargs.get( "database_connection", False ) self.database_engine_options = get_database_engine_options( kwargs ) self.database_create_tables = string_as_bool( kwargs.get( "database_create_tables", "True" ) ) + # Analytics + self.ga_code = kwargs.get( "ga_code", None ) # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/community_files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) diff -r d53d0150e936944c6a9e10dad1533a9645d37c48 -r 29a536155bf46e3c3dfa4f17760fda17f1e1835d templates/webapps/tool_shed/base_panels.mako --- a/templates/webapps/tool_shed/base_panels.mako +++ b/templates/webapps/tool_shed/base_panels.mako @@ -10,6 +10,17 @@ ## Masthead <%def name="masthead()"> + %if app.config.ga_code: + <script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + ga('create', '${app.config.ga_code}', 'auto'); + ga('send', 'pageview'); + </script> + %endif + ## start main tag <div id="masthead" class="navbar navbar-fixed-top navbar-inverse"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: Merged in martenson/galaxy-central-marten (pull request #548)
by commits-noreply＠bitbucket.org 04 Nov '14

04 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d53d0150e936/ Changeset: d53d0150e936 User: martenson Date: 2014-11-04 15:27:24+00:00 Summary: Merged in martenson/galaxy-central-marten (pull request #548) changesto user account updates Affected #: 2 files diff -r c7c9023e750ebae364c63345e59f2370f3f0905a -r d53d0150e936944c6a9e10dad1533a9645d37c48 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -573,7 +573,7 @@ email = trans.user.email if username is None: # User is coming from outside registration form, load email from trans username = trans.user.username - is_activation_sent = self.send_verification_email( trans, email, username) + is_activation_sent = self.send_verification_email( trans, email, username ) if is_activation_sent: message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address <b>%s</b> including the spam/trash folder.<br><a target="_top" href="%s">Return to the home page</a>.' % ( email, url_for( '/' ) ) status = 'error' @@ -819,7 +819,7 @@ def prepare_activation_link( self, trans, email ): """ - Prepares the account activation link for the user. + Prepare the account activation link for the user. """ activation_token = self.get_activation_token( trans, email ) activation_link = url_for( controller='user', action='activate', activation_token=activation_token, email=email, qualified=True ) @@ -827,7 +827,7 @@ def get_activation_token( self, trans, email ): """ - Checks for the activation token. Creates new activation token and stores it in the database if none found. + Check for the activation token. Create new activation token and store it in the database if no token found. """ user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() activation_token = user.activation_token @@ -841,7 +841,7 @@ @web.expose def activate( self, trans, **kwd ): """ - Function checks whether token fits the user and then activates the user's account. + Check whether token fits the user and then activate the user's account. """ params = util.Params( kwd, sanitize=False ) email = urllib.unquote( params.get( 'email', None ) ) @@ -849,7 +849,7 @@ if email is None or activation_token is None: # We don't have the email or activation_token, show error. - return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) + return trans.show_error_message( "You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) else: # Find the user user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() @@ -859,12 +859,12 @@ if user.activation_token == activation_token: user.activation_token = None user.active = True - trans.sa_session.add(user) + trans.sa_session.add( user ) trans.sa_session.flush() return trans.show_ok_message( "Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) else: # Tokens don't match. Activation is denied. - return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_error_message( "You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) return def __get_user_type_form_definition( self, trans, user=None, **kwd ): @@ -984,6 +984,9 @@ @web.expose def edit_info( self, trans, cntrller, **kwd ): + """ + Edit user information = username, email or password. + """ params = util.Params( kwd ) is_admin = cntrller == 'admin' and trans.user_is_admin() message = util.restore_text( params.get( 'message', '' ) ) @@ -1001,6 +1004,7 @@ # Editing email and username email = util.restore_text( params.get( 'email', '' ) ) username = util.restore_text( params.get( 'username', '' ) ).lower() + # Validate the new values for email and username message = validate_email( trans, email, user ) if not message and username: @@ -1008,15 +1012,32 @@ if message: status = 'error' else: - # The user's private role name must match the user's login ( email ) - private_role = trans.app.security_agent.get_private_user_role( user ) - private_role.name = email - private_role.description = 'Private role for ' + email - # Now change the user info - user.email = email - user.username = username - trans.sa_session.add_all( ( user, private_role ) ) - trans.sa_session.flush() + if ( user.email != email ): + # The user's private role name must match the user's login ( email ) + private_role = trans.app.security_agent.get_private_user_role( user ) + private_role.name = email + private_role.description = 'Private role for ' + email + # Change the email itself + user.email = email + trans.sa_session.add_all( ( user, private_role ) ) + trans.sa_session.flush() + if trans.webapp.name == 'galaxy' and trans.app.config.user_activation_on: + user.active = False + trans.sa_session.add( user ) + trans.sa_session.flush() + is_activation_sent = self.send_verification_email( trans, user.email, user.username ) + if is_activation_sent: + message = 'The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.' + success = True + else: + message = 'Unable to send activation email, please contact your local Galaxy administrator.' + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to + success = False + if ( user.username != username ): + user.username = username + trans.sa_session.add( user ) + trans.sa_session.flush() message = 'The login information has been updated with the changes.' elif user and params.get( 'change_password_button', False ): # Editing password. Do not sanitize passwords, so get from kwd @@ -1093,6 +1114,9 @@ @web.expose def reset_password( self, trans, email=None, **kwd ): + """ + Reset the user's password. Send him/her an email with the new password. + """ if trans.app.config.smtp_server is None: return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) message = util.sanitize_text(util.restore_text( kwd.get( 'message', '' ) )) @@ -1162,7 +1186,7 @@ @web.expose def set_default_permissions( self, trans, cntrller, **kwd ): - """Sets the user's default permissions for the new histories""" + """Set the user's default permissions for the new histories""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) diff -r c7c9023e750ebae364c63345e59f2370f3f0905a -r d53d0150e936944c6a9e10dad1533a9645d37c48 templates/user/info.mako --- a/templates/user/info.mako +++ b/templates/user/info.mako @@ -3,6 +3,80 @@ <% is_admin = cntrller == 'admin' and trans.user_is_admin() %><%def name="render_user_info()"> + + <script type="text/javascript"> + $(document).ready(function() { + + function validateString(test_string, type) { + var mail_re = /^(([^<>()[\]\\.,;:\s@\"]+(\.[^<>()[\]\\.,;:\s@\"]+)*)|(\".+\"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$/; + var username_re = /^[a-z0-9\-]{4,255}$/; + if (type === 'email') { + return mail_re.test(test_string); + } else if (type === 'username'){ + return username_re.test(test_string); + } + } + + function renderError(message) { + $(".donemessage").hide(); + if ($(".errormessage").length === 1) { + $(".errormessage").html(message); + } else { + var div = document.createElement( "div" ); + div.className = "errormessage"; + div.innerHTML = message; + document.body.insertBefore( div, document.body.firstChild ); + } + } + function renderDone(message) { + $(".errormessage").hide(); + if ($(".donemessage").length === 1) { + $(".donemessage").html(message); + } else { + var div = document.createElement( "div" ); + div.className = "donemessage"; + div.innerHTML = message; + document.body.insertBefore( div, document.body.firstChild ); + } + } + + original_email = $( '#email_input' ).val(); + original_username = $( '#name_input' ).val(); + + $( '#login_info' ).bind( 'submit', function( e ) { + var error_text_email= 'Please enter your valid email address.'; + var error_text_email_long= 'Email cannot be more than 255 characters in length.'; + var error_text_username_characters = 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 3.'; + var email = $( '#email_input' ).val(); + var name = $( '#name_input' ).val(); + var validForm = true; + var nothing_changed = ( original_email === email && original_username === name ); + // we need this value to detect submitting at backend + var hidden_input = '<input type="hidden" id="login_info_button" name="login_info_button" value="Submit"/>'; + $( '#send' ).attr( 'disabled', 'disabled' ); + $( "#email_input" ).before( hidden_input ); + + if ( original_email !== email ){ + if ( email.length > 255 ){ renderError( error_text_email_long ); validForm = false; } + else if ( !validateString( email, "email" ) ){ renderError( error_text_email ); validForm = false; } + } + if ( original_username !== name ){ + if ( name && !( validateString( name,"username" ) ) ){ renderError( error_text_username_characters ); validForm = false; } + } + if ( nothing_changed ){ + renderDone( "Nothing has changed." ); + } + if ( !validForm || nothing_changed ) { + e.preventDefault(); + // reactivate the button if the form wasn't submitted + $( '#send' ).removeAttr( 'disabled' ); + } + }); + }); + + </script> + + <h2>Manage User Information</h2> %if not is_admin: <ul class="manage-table-actions"> @@ -16,7 +90,10 @@ <div class="toolFormTitle">Login Information</div><div class="form-row"><label>Email address:</label> - <input type="text" name="email" value="${email}" size="40"/> + <input type="text" id ="email_input" name="email" value="${email}" size="40"/> + <div class="toolParamHelp" style="clear: both;"> + If you change your email address you will receive an activation link in the new mailbox and you have to activate your account by visiting it. + </div></div><div class="form-row"><label>Public name:</label> @@ -37,7 +114,7 @@ </div> %endif %else: - <input type="text" name="username" size="40" value="${username}"/> + <input type="text" id="name_input" name="username" size="40" value="${username}"/><div class="toolParamHelp" style="clear: both;"> Your public name is an optional identifier that will be used to generate addresses for information you share publicly. Public names must be at least four characters in length and contain only lower-case @@ -46,7 +123,7 @@ %endif </div><div class="form-row"> - <input type="submit" name="login_info_button" value="Save"/> + <input type="submit" id="send" name="login_info_button" value="Save"/></div></form></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 04 Nov '14

04 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43bf2d91ca84/ Changeset: 43bf2d91ca84 User: martenson Date: 2014-11-03 20:16:36+00:00 Summary: changes to account updates: added javascript valdiation of username and email changes; user account will be deactivated if you change an email address and you have to activate it once again Affected #: 2 files diff -r db6130ed74cd2186e8646e20a8c94993c114ff1a -r 43bf2d91ca84df43bea0c0dc9c8b5b1e1f4098b6 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -573,7 +573,7 @@ email = trans.user.email if username is None: # User is coming from outside registration form, load email from trans username = trans.user.username - is_activation_sent = self.send_verification_email( trans, email, username) + is_activation_sent = self.send_verification_email( trans, email, username ) if is_activation_sent: message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address <b>%s</b> including the spam/trash folder.<br><a target="_top" href="%s">Return to the home page</a>.' % ( email, url_for( '/' ) ) status = 'error' @@ -819,7 +819,7 @@ def prepare_activation_link( self, trans, email ): """ - Prepares the account activation link for the user. + Prepare the account activation link for the user. """ activation_token = self.get_activation_token( trans, email ) activation_link = url_for( controller='user', action='activate', activation_token=activation_token, email=email, qualified=True ) @@ -827,7 +827,7 @@ def get_activation_token( self, trans, email ): """ - Checks for the activation token. Creates new activation token and stores it in the database if none found. + Check for the activation token. Create new activation token and store it in the database if no token found. """ user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() activation_token = user.activation_token @@ -841,7 +841,7 @@ @web.expose def activate( self, trans, **kwd ): """ - Function checks whether token fits the user and then activates the user's account. + Check whether token fits the user and then activate the user's account. """ params = util.Params( kwd, sanitize=False ) email = urllib.unquote( params.get( 'email', None ) ) @@ -849,7 +849,7 @@ if email is None or activation_token is None: # We don't have the email or activation_token, show error. - return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) + return trans.show_error_message( "You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) else: # Find the user user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() @@ -859,12 +859,12 @@ if user.activation_token == activation_token: user.activation_token = None user.active = True - trans.sa_session.add(user) + trans.sa_session.add( user ) trans.sa_session.flush() return trans.show_ok_message( "Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) else: # Tokens don't match. Activation is denied. - return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_error_message( "You are using invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) return def __get_user_type_form_definition( self, trans, user=None, **kwd ): @@ -984,6 +984,9 @@ @web.expose def edit_info( self, trans, cntrller, **kwd ): + """ + Edit user information = username, email or password. + """ params = util.Params( kwd ) is_admin = cntrller == 'admin' and trans.user_is_admin() message = util.restore_text( params.get( 'message', '' ) ) @@ -1001,6 +1004,7 @@ # Editing email and username email = util.restore_text( params.get( 'email', '' ) ) username = util.restore_text( params.get( 'username', '' ) ).lower() + # Validate the new values for email and username message = validate_email( trans, email, user ) if not message and username: @@ -1008,15 +1012,32 @@ if message: status = 'error' else: - # The user's private role name must match the user's login ( email ) - private_role = trans.app.security_agent.get_private_user_role( user ) - private_role.name = email - private_role.description = 'Private role for ' + email - # Now change the user info - user.email = email - user.username = username - trans.sa_session.add_all( ( user, private_role ) ) - trans.sa_session.flush() + if ( user.email != email ): + # The user's private role name must match the user's login ( email ) + private_role = trans.app.security_agent.get_private_user_role( user ) + private_role.name = email + private_role.description = 'Private role for ' + email + # Change the email itself + user.email = email + trans.sa_session.add_all( ( user, private_role ) ) + trans.sa_session.flush() + if trans.webapp.name == 'galaxy' and trans.app.config.user_activation_on: + user.active = False + trans.sa_session.add( user ) + trans.sa_session.flush() + is_activation_sent = self.send_verification_email( trans, user.email, user.username ) + if is_activation_sent: + message = 'The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.' + success = True + else: + message = 'Unable to send activation email, please contact your local Galaxy administrator.' + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to + success = False + if ( user.username != username ): + user.username = username + trans.sa_session.add( user ) + trans.sa_session.flush() message = 'The login information has been updated with the changes.' elif user and params.get( 'change_password_button', False ): # Editing password. Do not sanitize passwords, so get from kwd @@ -1093,6 +1114,9 @@ @web.expose def reset_password( self, trans, email=None, **kwd ): + """ + Reset the user's password. Send him/her an email with the new password. + """ if trans.app.config.smtp_server is None: return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) message = util.sanitize_text(util.restore_text( kwd.get( 'message', '' ) )) @@ -1162,7 +1186,7 @@ @web.expose def set_default_permissions( self, trans, cntrller, **kwd ): - """Sets the user's default permissions for the new histories""" + """Set the user's default permissions for the new histories""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) diff -r db6130ed74cd2186e8646e20a8c94993c114ff1a -r 43bf2d91ca84df43bea0c0dc9c8b5b1e1f4098b6 templates/user/info.mako --- a/templates/user/info.mako +++ b/templates/user/info.mako @@ -3,6 +3,80 @@ <% is_admin = cntrller == 'admin' and trans.user_is_admin() %><%def name="render_user_info()"> + + <script type="text/javascript"> + $(document).ready(function() { + + function validateString(test_string, type) { + var mail_re = /^(([^<>()[\]\\.,;:\s@\"]+(\.[^<>()[\]\\.,;:\s@\"]+)*)|(\".+\"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$/; + var username_re = /^[a-z0-9\-]{4,255}$/; + if (type === 'email') { + return mail_re.test(test_string); + } else if (type === 'username'){ + return username_re.test(test_string); + } + } + + function renderError(message) { + $(".donemessage").hide(); + if ($(".errormessage").length === 1) { + $(".errormessage").html(message); + } else { + var div = document.createElement( "div" ); + div.className = "errormessage"; + div.innerHTML = message; + document.body.insertBefore( div, document.body.firstChild ); + } + } + function renderDone(message) { + $(".errormessage").hide(); + if ($(".donemessage").length === 1) { + $(".donemessage").html(message); + } else { + var div = document.createElement( "div" ); + div.className = "donemessage"; + div.innerHTML = message; + document.body.insertBefore( div, document.body.firstChild ); + } + } + + original_email = $( '#email_input' ).val(); + original_username = $( '#name_input' ).val(); + + $( '#login_info' ).bind( 'submit', function( e ) { + var error_text_email= 'Please enter your valid email address.'; + var error_text_email_long= 'Email cannot be more than 255 characters in length.'; + var error_text_username_characters = 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 3.'; + var email = $( '#email_input' ).val(); + var name = $( '#name_input' ).val(); + var validForm = true; + var nothing_changed = ( original_email === email && original_username === name ); + // we need this value to detect submitting at backend + var hidden_input = '<input type="hidden" id="login_info_button" name="login_info_button" value="Submit"/>'; + $( '#send' ).attr( 'disabled', 'disabled' ); + $( "#email_input" ).before( hidden_input ); + + if ( original_email !== email ){ + if ( email.length > 255 ){ renderError( error_text_email_long ); validForm = false; } + else if ( !validateString( email, "email" ) ){ renderError( error_text_email ); validForm = false; } + } + if ( original_username !== name ){ + if ( name && !( validateString( name,"username" ) ) ){ renderError( error_text_username_characters ); validForm = false; } + } + if ( nothing_changed ){ + renderDone( "Nothing has changed." ); + } + if ( !validForm || nothing_changed ) { + e.preventDefault(); + // reactivate the button if the form wasn't submitted + $( '#send' ).removeAttr( 'disabled' ); + } + }); + }); + + </script> + + <h2>Manage User Information</h2> %if not is_admin: <ul class="manage-table-actions"> @@ -16,7 +90,10 @@ <div class="toolFormTitle">Login Information</div><div class="form-row"><label>Email address:</label> - <input type="text" name="email" value="${email}" size="40"/> + <input type="text" id ="email_input" name="email" value="${email}" size="40"/> + <div class="toolParamHelp" style="clear: both;"> + If you change your email address you will receive an activation link in the new mailbox and you have to activate your account by visiting it. + </div></div><div class="form-row"><label>Public name:</label> @@ -37,7 +114,7 @@ </div> %endif %else: - <input type="text" name="username" size="40" value="${username}"/> + <input type="text" id="name_input" name="username" size="40" value="${username}"/><div class="toolParamHelp" style="clear: both;"> Your public name is an optional identifier that will be used to generate addresses for information you share publicly. Public names must be at least four characters in length and contain only lower-case @@ -46,7 +123,7 @@ %endif </div><div class="form-row"> - <input type="submit" name="login_info_button" value="Save"/> + <input type="submit" id="send" name="login_info_button" value="Save"/></div></form></div> https://bitbucket.org/galaxy/galaxy-central/commits/ef99f015a0d2/ Changeset: ef99f015a0d2 User: martenson Date: 2014-11-04 15:26:53+00:00 Summary: gremmar Affected #: 1 file diff -r 43bf2d91ca84df43bea0c0dc9c8b5b1e1f4098b6 -r ef99f015a0d2100e3c3e139ddf3dbf7d5ca6a299 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -864,7 +864,7 @@ return trans.show_ok_message( "Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) else: # Tokens don't match. Activation is denied. - return trans.show_error_message( "You are using invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_error_message( "You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) return def __get_user_type_form_definition( self, trans, user=None, **kwd ): https://bitbucket.org/galaxy/galaxy-central/commits/d53d0150e936/ Changeset: d53d0150e936 User: martenson Date: 2014-11-04 15:27:24+00:00 Summary: Merged in martenson/galaxy-central-marten (pull request #548) changesto user account updates Affected #: 2 files diff -r c7c9023e750ebae364c63345e59f2370f3f0905a -r d53d0150e936944c6a9e10dad1533a9645d37c48 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -573,7 +573,7 @@ email = trans.user.email if username is None: # User is coming from outside registration form, load email from trans username = trans.user.username - is_activation_sent = self.send_verification_email( trans, email, username) + is_activation_sent = self.send_verification_email( trans, email, username ) if is_activation_sent: message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address <b>%s</b> including the spam/trash folder.<br><a target="_top" href="%s">Return to the home page</a>.' % ( email, url_for( '/' ) ) status = 'error' @@ -819,7 +819,7 @@ def prepare_activation_link( self, trans, email ): """ - Prepares the account activation link for the user. + Prepare the account activation link for the user. """ activation_token = self.get_activation_token( trans, email ) activation_link = url_for( controller='user', action='activate', activation_token=activation_token, email=email, qualified=True ) @@ -827,7 +827,7 @@ def get_activation_token( self, trans, email ): """ - Checks for the activation token. Creates new activation token and stores it in the database if none found. + Check for the activation token. Create new activation token and store it in the database if no token found. """ user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() activation_token = user.activation_token @@ -841,7 +841,7 @@ @web.expose def activate( self, trans, **kwd ): """ - Function checks whether token fits the user and then activates the user's account. + Check whether token fits the user and then activate the user's account. """ params = util.Params( kwd, sanitize=False ) email = urllib.unquote( params.get( 'email', None ) ) @@ -849,7 +849,7 @@ if email is None or activation_token is None: # We don't have the email or activation_token, show error. - return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) + return trans.show_error_message( "You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) else: # Find the user user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() @@ -859,12 +859,12 @@ if user.activation_token == activation_token: user.activation_token = None user.active = True - trans.sa_session.add(user) + trans.sa_session.add( user ) trans.sa_session.flush() return trans.show_ok_message( "Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) else: # Tokens don't match. Activation is denied. - return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_error_message( "You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) return def __get_user_type_form_definition( self, trans, user=None, **kwd ): @@ -984,6 +984,9 @@ @web.expose def edit_info( self, trans, cntrller, **kwd ): + """ + Edit user information = username, email or password. + """ params = util.Params( kwd ) is_admin = cntrller == 'admin' and trans.user_is_admin() message = util.restore_text( params.get( 'message', '' ) ) @@ -1001,6 +1004,7 @@ # Editing email and username email = util.restore_text( params.get( 'email', '' ) ) username = util.restore_text( params.get( 'username', '' ) ).lower() + # Validate the new values for email and username message = validate_email( trans, email, user ) if not message and username: @@ -1008,15 +1012,32 @@ if message: status = 'error' else: - # The user's private role name must match the user's login ( email ) - private_role = trans.app.security_agent.get_private_user_role( user ) - private_role.name = email - private_role.description = 'Private role for ' + email - # Now change the user info - user.email = email - user.username = username - trans.sa_session.add_all( ( user, private_role ) ) - trans.sa_session.flush() + if ( user.email != email ): + # The user's private role name must match the user's login ( email ) + private_role = trans.app.security_agent.get_private_user_role( user ) + private_role.name = email + private_role.description = 'Private role for ' + email + # Change the email itself + user.email = email + trans.sa_session.add_all( ( user, private_role ) ) + trans.sa_session.flush() + if trans.webapp.name == 'galaxy' and trans.app.config.user_activation_on: + user.active = False + trans.sa_session.add( user ) + trans.sa_session.flush() + is_activation_sent = self.send_verification_email( trans, user.email, user.username ) + if is_activation_sent: + message = 'The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.' + success = True + else: + message = 'Unable to send activation email, please contact your local Galaxy administrator.' + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to + success = False + if ( user.username != username ): + user.username = username + trans.sa_session.add( user ) + trans.sa_session.flush() message = 'The login information has been updated with the changes.' elif user and params.get( 'change_password_button', False ): # Editing password. Do not sanitize passwords, so get from kwd @@ -1093,6 +1114,9 @@ @web.expose def reset_password( self, trans, email=None, **kwd ): + """ + Reset the user's password. Send him/her an email with the new password. + """ if trans.app.config.smtp_server is None: return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) message = util.sanitize_text(util.restore_text( kwd.get( 'message', '' ) )) @@ -1162,7 +1186,7 @@ @web.expose def set_default_permissions( self, trans, cntrller, **kwd ): - """Sets the user's default permissions for the new histories""" + """Set the user's default permissions for the new histories""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) diff -r c7c9023e750ebae364c63345e59f2370f3f0905a -r d53d0150e936944c6a9e10dad1533a9645d37c48 templates/user/info.mako --- a/templates/user/info.mako +++ b/templates/user/info.mako @@ -3,6 +3,80 @@ <% is_admin = cntrller == 'admin' and trans.user_is_admin() %><%def name="render_user_info()"> + + <script type="text/javascript"> + $(document).ready(function() { + + function validateString(test_string, type) { + var mail_re = /^(([^<>()[\]\\.,;:\s@\"]+(\.[^<>()[\]\\.,;:\s@\"]+)*)|(\".+\"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$/; + var username_re = /^[a-z0-9\-]{4,255}$/; + if (type === 'email') { + return mail_re.test(test_string); + } else if (type === 'username'){ + return username_re.test(test_string); + } + } + + function renderError(message) { + $(".donemessage").hide(); + if ($(".errormessage").length === 1) { + $(".errormessage").html(message); + } else { + var div = document.createElement( "div" ); + div.className = "errormessage"; + div.innerHTML = message; + document.body.insertBefore( div, document.body.firstChild ); + } + } + function renderDone(message) { + $(".errormessage").hide(); + if ($(".donemessage").length === 1) { + $(".donemessage").html(message); + } else { + var div = document.createElement( "div" ); + div.className = "donemessage"; + div.innerHTML = message; + document.body.insertBefore( div, document.body.firstChild ); + } + } + + original_email = $( '#email_input' ).val(); + original_username = $( '#name_input' ).val(); + + $( '#login_info' ).bind( 'submit', function( e ) { + var error_text_email= 'Please enter your valid email address.'; + var error_text_email_long= 'Email cannot be more than 255 characters in length.'; + var error_text_username_characters = 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 3.'; + var email = $( '#email_input' ).val(); + var name = $( '#name_input' ).val(); + var validForm = true; + var nothing_changed = ( original_email === email && original_username === name ); + // we need this value to detect submitting at backend + var hidden_input = '<input type="hidden" id="login_info_button" name="login_info_button" value="Submit"/>'; + $( '#send' ).attr( 'disabled', 'disabled' ); + $( "#email_input" ).before( hidden_input ); + + if ( original_email !== email ){ + if ( email.length > 255 ){ renderError( error_text_email_long ); validForm = false; } + else if ( !validateString( email, "email" ) ){ renderError( error_text_email ); validForm = false; } + } + if ( original_username !== name ){ + if ( name && !( validateString( name,"username" ) ) ){ renderError( error_text_username_characters ); validForm = false; } + } + if ( nothing_changed ){ + renderDone( "Nothing has changed." ); + } + if ( !validForm || nothing_changed ) { + e.preventDefault(); + // reactivate the button if the form wasn't submitted + $( '#send' ).removeAttr( 'disabled' ); + } + }); + }); + + </script> + + <h2>Manage User Information</h2> %if not is_admin: <ul class="manage-table-actions"> @@ -16,7 +90,10 @@ <div class="toolFormTitle">Login Information</div><div class="form-row"><label>Email address:</label> - <input type="text" name="email" value="${email}" size="40"/> + <input type="text" id ="email_input" name="email" value="${email}" size="40"/> + <div class="toolParamHelp" style="clear: both;"> + If you change your email address you will receive an activation link in the new mailbox and you have to activate your account by visiting it. + </div></div><div class="form-row"><label>Public name:</label> @@ -37,7 +114,7 @@ </div> %endif %else: - <input type="text" name="username" size="40" value="${username}"/> + <input type="text" id="name_input" name="username" size="40" value="${username}"/><div class="toolParamHelp" style="clear: both;"> Your public name is an optional identifier that will be used to generate addresses for information you share publicly. Public names must be at least four characters in length and contain only lower-case @@ -46,7 +123,7 @@ %endif </div><div class="form-row"> - <input type="submit" name="login_info_button" value="Save"/> + <input type="submit" id="send" name="login_info_button" value="Save"/></div></form></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Merge default
by commits-noreply＠bitbucket.org 04 Nov '14

04 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c7c9023e750e/ Changeset: c7c9023e750e User: carlfeberhard Date: 2014-11-04 15:15:08+00:00 Summary: Merge default Affected #: 3 files diff -r db6130ed74cd2186e8646e20a8c94993c114ff1a -r c7c9023e750ebae364c63345e59f2370f3f0905a client/galaxy/scripts/mvc/dataset/dataset-model.js --- a/client/galaxy/scripts/mvc/dataset/dataset-model.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-model.js @@ -94,10 +94,7 @@ this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); } }); - this.on( 'change:urls', function(){ - console.warn( 'change:urls', arguments ); - }); - // the download url (currenlty) relies on having a correct file extension + // the download url (currently) relies on having a correct file extension this.on( 'change:id change:file_ext', function( currModel ){ this._generateUrls(); }); @@ -139,8 +136,15 @@ }, // ........................................................................ ajax + fetch : function( options ){ + var dataset = this; + return Backbone.Model.prototype.fetch.call( this, options ) + .always( function(){ + dataset._generateUrls(); + }); + }, + //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly - /** save this dataset, _Mark_ing it as deleted (just a flag) */ 'delete' : function( options ){ if( this.get( 'deleted' ) ){ return jQuery.when(); } diff -r db6130ed74cd2186e8646e20a8c94993c114ff1a -r c7c9023e750ebae364c63345e59f2370f3f0905a static/scripts/mvc/dataset/dataset-model.js --- a/static/scripts/mvc/dataset/dataset-model.js +++ b/static/scripts/mvc/dataset/dataset-model.js @@ -94,10 +94,7 @@ this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); } }); - this.on( 'change:urls', function(){ - console.warn( 'change:urls', arguments ); - }); - // the download url (currenlty) relies on having a correct file extension + // the download url (currently) relies on having a correct file extension this.on( 'change:id change:file_ext', function( currModel ){ this._generateUrls(); }); @@ -139,8 +136,15 @@ }, // ........................................................................ ajax + fetch : function( options ){ + var dataset = this; + return Backbone.Model.prototype.fetch.call( this, options ) + .always( function(){ + dataset._generateUrls(); + }); + }, + //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly - /** save this dataset, _Mark_ing it as deleted (just a flag) */ 'delete' : function( options ){ if( this.get( 'deleted' ) ){ return jQuery.when(); } diff -r db6130ed74cd2186e8646e20a8c94993c114ff1a -r c7c9023e750ebae364c63345e59f2370f3f0905a static/scripts/packed/mvc/dataset/dataset-model.js --- a/static/scripts/packed/mvc/dataset/dataset-model.js +++ b/static/scripts/packed/mvc/dataset/dataset-model.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,d){var g=b.SearchableModelMixin;var f=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(g,{defaults:{state:a.NEW,deleted:false,purged:false,name:"(unnamed dataset)",accessible:true,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(h,i){this.debug(this+"(Dataset).initialize",h,i);if(!this.get("accessible")){this.set("state",a.NOT_VIEWABLE)}this.urls=this._generateUrls();this._setUpListeners()},_generateUrls:function(){var j=this.get("id");if(!j){return{}}var i={purge:"datasets/"+j+"/purge_async",display:"datasets/"+j+"/display/?preview=True",edit:"datasets/"+j+"/edit",download:"datasets/"+j+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+j,rerun:"tool_runner/rerun?id="+j,show_params:"datasets/"+j+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+j+"&metadata_name="};var h=(window.galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/");_.each(i,function(l,k){i[k]=h+l});this.urls=i;return i},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}});this.on("change:urls",function(){console.warn("change:urls",arguments)});this.on("change:id change:file_ext",function(h){this._generateUrls()})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);return _.extend(h,{urls:this.urls})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var h=_.contains(a.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function(h){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},h)},undelete:function(h){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},h)},purge:function e(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=this.urls.purge;var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=d("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,d(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var h=this.get("id")||"";if(this.get("name")){h='"'+this.get("name")+'",'+h}return"Dataset("+h+")"}}));var c=Backbone.Collection.extend(b.LoggableMixin).extend({model:f,urlRoot:((window.galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/"))+"api/datasets",ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){if(!i.get(l.id)){return l}var k=existing.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["DatasetAssociationCollection(",this.length,")"].join(""))}});return{DatasetAssociation:f,DatasetAssociationCollection:c}}); \ No newline at end of file +define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,d){var g=b.SearchableModelMixin;var f=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(g,{defaults:{state:a.NEW,deleted:false,purged:false,name:"(unnamed dataset)",accessible:true,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(h,i){this.debug(this+"(Dataset).initialize",h,i);if(!this.get("accessible")){this.set("state",a.NOT_VIEWABLE)}this.urls=this._generateUrls();this._setUpListeners()},_generateUrls:function(){var j=this.get("id");if(!j){return{}}var i={purge:"datasets/"+j+"/purge_async",display:"datasets/"+j+"/display/?preview=True",edit:"datasets/"+j+"/edit",download:"datasets/"+j+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+j,rerun:"tool_runner/rerun?id="+j,show_params:"datasets/"+j+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+j+"&metadata_name="};var h=(window.galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/");_.each(i,function(l,k){i[k]=h+l});this.urls=i;return i},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}});this.on("change:id change:file_ext",function(h){this._generateUrls()})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);return _.extend(h,{urls:this.urls})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var h=_.contains(a.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},fetch:function(h){var i=this;return Backbone.Model.prototype.fetch.call(this,h).always(function(){i._generateUrls()})},"delete":function(h){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},h)},undelete:function(h){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},h)},purge:function e(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=this.urls.purge;var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=d("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,d(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var h=this.get("id")||"";if(this.get("name")){h='"'+this.get("name")+'",'+h}return"Dataset("+h+")"}}));var c=Backbone.Collection.extend(b.LoggableMixin).extend({model:f,urlRoot:((window.galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/"))+"api/datasets",ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){if(!i.get(l.id)){return l}var k=existing.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["DatasetAssociationCollection(",this.length,")"].join(""))}});return{DatasetAssociation:f,DatasetAssociationCollection:c}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fix: regenerate dataset-model urls on fetch even when silent
by commits-noreply＠bitbucket.org 04 Nov '14

04 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b8cb8d48a79/ Changeset: 9b8cb8d48a79 Branch: stable User: carlfeberhard Date: 2014-11-04 14:51:53+00:00 Summary: Fix: regenerate dataset-model urls on fetch even when silent Affected #: 3 files diff -r 5123ed7f16037c67a66f90ce63ef5a15faab21c9 -r 9b8cb8d48a798e8905d09e380138c1102012ce6f client/galaxy/scripts/mvc/dataset/dataset-model.js --- a/client/galaxy/scripts/mvc/dataset/dataset-model.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-model.js @@ -94,10 +94,7 @@ this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); } }); - this.on( 'change:urls', function(){ - console.warn( 'change:urls', arguments ); - }); - // the download url (currenlty) relies on having a correct file extension + // the download url (currently) relies on having a correct file extension this.on( 'change:id change:file_ext', function( currModel ){ this._generateUrls(); }); @@ -139,8 +136,15 @@ }, // ........................................................................ ajax + fetch : function( options ){ + var dataset = this; + return Backbone.Model.prototype.fetch.call( this, options ) + .always( function(){ + dataset._generateUrls(); + }); + }, + //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly - /** save this dataset, _Mark_ing it as deleted (just a flag) */ 'delete' : function( options ){ if( this.get( 'deleted' ) ){ return jQuery.when(); } diff -r 5123ed7f16037c67a66f90ce63ef5a15faab21c9 -r 9b8cb8d48a798e8905d09e380138c1102012ce6f static/scripts/mvc/dataset/dataset-model.js --- a/static/scripts/mvc/dataset/dataset-model.js +++ b/static/scripts/mvc/dataset/dataset-model.js @@ -94,10 +94,7 @@ this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); } }); - this.on( 'change:urls', function(){ - console.warn( 'change:urls', arguments ); - }); - // the download url (currenlty) relies on having a correct file extension + // the download url (currently) relies on having a correct file extension this.on( 'change:id change:file_ext', function( currModel ){ this._generateUrls(); }); @@ -139,8 +136,15 @@ }, // ........................................................................ ajax + fetch : function( options ){ + var dataset = this; + return Backbone.Model.prototype.fetch.call( this, options ) + .always( function(){ + dataset._generateUrls(); + }); + }, + //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly - /** save this dataset, _Mark_ing it as deleted (just a flag) */ 'delete' : function( options ){ if( this.get( 'deleted' ) ){ return jQuery.when(); } diff -r 5123ed7f16037c67a66f90ce63ef5a15faab21c9 -r 9b8cb8d48a798e8905d09e380138c1102012ce6f static/scripts/packed/mvc/dataset/dataset-model.js --- a/static/scripts/packed/mvc/dataset/dataset-model.js +++ b/static/scripts/packed/mvc/dataset/dataset-model.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,d){var g=b.SearchableModelMixin;var f=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(g,{defaults:{state:a.NEW,deleted:false,purged:false,name:"(unnamed dataset)",accessible:true,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(h,i){this.debug(this+"(Dataset).initialize",h,i);if(!this.get("accessible")){this.set("state",a.NOT_VIEWABLE)}this.urls=this._generateUrls();this._setUpListeners()},_generateUrls:function(){var j=this.get("id");if(!j){return{}}var i={purge:"datasets/"+j+"/purge_async",display:"datasets/"+j+"/display/?preview=True",edit:"datasets/"+j+"/edit",download:"datasets/"+j+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+j,rerun:"tool_runner/rerun?id="+j,show_params:"datasets/"+j+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+j+"&metadata_name="};var h=(window.galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/");_.each(i,function(l,k){i[k]=h+l});this.urls=i;return i},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}});this.on("change:urls",function(){console.warn("change:urls",arguments)});this.on("change:id change:file_ext",function(h){this._generateUrls()})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);return _.extend(h,{urls:this.urls})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var h=_.contains(a.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function(h){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},h)},undelete:function(h){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},h)},purge:function e(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=this.urls.purge;var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=d("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,d(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var h=this.get("id")||"";if(this.get("name")){h='"'+this.get("name")+'",'+h}return"Dataset("+h+")"}}));var c=Backbone.Collection.extend(b.LoggableMixin).extend({model:f,urlRoot:((window.galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/"))+"api/datasets",ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){if(!i.get(l.id)){return l}var k=existing.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["DatasetAssociationCollection(",this.length,")"].join(""))}});return{DatasetAssociation:f,DatasetAssociationCollection:c}}); \ No newline at end of file +define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,d){var g=b.SearchableModelMixin;var f=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(g,{defaults:{state:a.NEW,deleted:false,purged:false,name:"(unnamed dataset)",accessible:true,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(h,i){this.debug(this+"(Dataset).initialize",h,i);if(!this.get("accessible")){this.set("state",a.NOT_VIEWABLE)}this.urls=this._generateUrls();this._setUpListeners()},_generateUrls:function(){var j=this.get("id");if(!j){return{}}var i={purge:"datasets/"+j+"/purge_async",display:"datasets/"+j+"/display/?preview=True",edit:"datasets/"+j+"/edit",download:"datasets/"+j+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+j,rerun:"tool_runner/rerun?id="+j,show_params:"datasets/"+j+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+j+"&metadata_name="};var h=(window.galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/");_.each(i,function(l,k){i[k]=h+l});this.urls=i;return i},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}});this.on("change:id change:file_ext",function(h){this._generateUrls()})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);return _.extend(h,{urls:this.urls})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var h=_.contains(a.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},fetch:function(h){var i=this;return Backbone.Model.prototype.fetch.call(this,h).always(function(){i._generateUrls()})},"delete":function(h){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},h)},undelete:function(h){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},h)},purge:function e(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=this.urls.purge;var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=d("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,d(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var h=this.get("id")||"";if(this.get("name")){h='"'+this.get("name")+'",'+h}return"Dataset("+h+")"}}));var c=Backbone.Collection.extend(b.LoggableMixin).extend({model:f,urlRoot:((window.galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/"))+"api/datasets",ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){if(!i.get(l.id)){return l}var k=existing.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["DatasetAssociationCollection(",this.length,")"].join(""))}});return{DatasetAssociation:f,DatasetAssociationCollection:c}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 03 Nov '14

03 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1370ef01209d/ Changeset: 1370ef01209d User: dannon Date: 2014-11-03 19:52:21+00:00 Summary: Patch from Eric Rasche, redacting a few things from sentry reports. Affected #: 1 file diff -r 1bb61cbf80825b0793a61d83f01925b57467d3a9 -r 1370ef01209d6b6329c9285891e94ebd2f7ccdb6 lib/galaxy/web/framework/middleware/sentry.py --- a/lib/galaxy/web/framework/middleware/sentry.py +++ b/lib/galaxy/web/framework/middleware/sentry.py @@ -44,6 +44,25 @@ self.handle_exception(environ) def handle_exception(self, environ): + headers = dict(get_headers(environ)) + # Authorization header for REMOTE_USER sites consists of a base64() of + # their plaintext password. It is a security issue for this password to + # be exposed to a third party system which may or may not be under + # control of the same administrators as the local Authentication + # system. E.g. university LDAP systems. + if 'Authorization' in headers: + # Redact so the administrator knows that a value is indeed present. + headers['Authorization'] = 'redacted' + # Passing cookies allows for impersonation of users (depending on + # remote service) and can be considered a security risk as well. For + # multiple services running alongside Galaxy on the same host, this + # could allow a sentry user with access to logs to impersonate a user + # on another service. In the case of services like IPython, this can be + # a serious concern as that would allow for terminal access. Furthermore, + # very little debugging information can be gained as a result of having + # access to all of the users cookies (including Galaxy cookies) + if 'Cookie' in headers: + headers['Cookie'] = 'redacted' event_id = self.client.captureException( data={ 'sentry.interfaces.Http': { @@ -52,7 +71,7 @@ 'query_string': environ.get('QUERY_STRING'), # TODO # 'data': environ.get('wsgi.input'), - 'headers': dict(get_headers(environ)), + 'headers': headers, 'env': dict(get_environ(environ)), } }, https://bitbucket.org/galaxy/galaxy-central/commits/db6130ed74cd/ Changeset: db6130ed74cd User: dannon Date: 2014-11-03 20:04:17+00:00 Summary: Merge. Affected #: 2 files diff -r 1370ef01209d6b6329c9285891e94ebd2f7ccdb6 -r db6130ed74cd2186e8646e20a8c94993c114ff1a lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -362,6 +362,11 @@ try: # Substituting parameters into the command command_line = fill_template( command, context=param_dict ) + cleaned_command_line = [] + # Remove leading and trailing whitespace from each line for readability. + for line in command_line.split( '\n' ): + cleaned_command_line.append( line.strip() ) + command_line = '\n'.join( cleaned_command_line ) # Remove newlines from command line, and any leading/trailing white space command_line = command_line.replace( "\n", " " ).replace( "\r", " " ).strip() except Exception: diff -r 1370ef01209d6b6329c9285891e94ebd2f7ccdb6 -r db6130ed74cd2186e8646e20a8c94993c114ff1a test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -441,7 +441,9 @@ pass print "Database connection: ", database_connection print "Install database connection: ", install_database_connection - # Generate the shed_tool_data_table_conf.xml file. + # Generate the tool data table configuration files. + if not os.path.exists( galaxy_tool_data_table_conf_file ): + file( galaxy_tool_data_table_conf_file, 'w' ).write( install_and_test_base_util.tool_data_table_conf_xml_template ) file( shed_tool_data_table_conf_file, 'w' ).write( install_and_test_base_util.tool_data_table_conf_xml_template ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file # ---- Start up a Galaxy instance ------------------------------------------------------ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 03 Nov '14

03 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eacea367580f/ Changeset: eacea367580f User: davebgx Date: 2014-10-30 15:30:46+00:00 Summary: Remove whitespace from the beginning and end of individual lines in a <command> tag before assembling it into a single line. Affected #: 1 file diff -r 713526cf328d41f0248ce85860e1d33db779482f -r eacea367580f33e7515752cc598d8ed170393685 lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -362,6 +362,11 @@ try: # Substituting parameters into the command command_line = fill_template( command, context=param_dict ) + cleaned_command_line = [] + # Remove leading and trailing whitespace from each line for readability. + for line in command_line.split( '\n' ): + cleaned_command_line.append( line.strip() ) + command_line = '\n'.join( cleaned_command_line ) # Remove newlines from command line, and any leading/trailing white space command_line = command_line.replace( "\n", " " ).replace( "\r", " " ).strip() except Exception: https://bitbucket.org/galaxy/galaxy-central/commits/6e6867f885b3/ Changeset: 6e6867f885b3 User: davebgx Date: 2014-11-03 19:58:35+00:00 Summary: Create the tool_data_table_conf.xml file if it doesn't exist Affected #: 1 file diff -r eacea367580f33e7515752cc598d8ed170393685 -r 6e6867f885b36321be98635c50c2279fc88c8fd0 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -441,7 +441,9 @@ pass print "Database connection: ", database_connection print "Install database connection: ", install_database_connection - # Generate the shed_tool_data_table_conf.xml file. + # Generate the tool data table configuration files. + if not os.path.exists( galaxy_tool_data_table_conf_file ): + file( galaxy_tool_data_table_conf_file, 'w' ).write( install_and_test_base_util.tool_data_table_conf_xml_template ) file( shed_tool_data_table_conf_file, 'w' ).write( install_and_test_base_util.tool_data_table_conf_xml_template ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file # ---- Start up a Galaxy instance ------------------------------------------------------ https://bitbucket.org/galaxy/galaxy-central/commits/09e676cbd155/ Changeset: 09e676cbd155 User: davebgx Date: 2014-11-03 19:59:16+00:00 Summary: Merge with upstream changes. Affected #: 33 files diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -64,18 +64,76 @@ } }, - // refresh + // rebuild underlying data structure representation for the tool form + // this happens i.e. when repeat blocks are added or removed and on initialization + rebuild: function() { + this.tree.refresh(); + console.debug('tools-form::refresh() - Refreshed form structure.'); + }, + + // refreshes input states i.e. for dynamic parameters refresh: function() { - // recreate tree structure - this.tree.refresh(); + // link this + var self = this; - // trigger change - for (var id in this.field_list) { - this.field_list[id].trigger('change'); + // only refresh the state if the form contains dynamic parameters + if (!this.is_dynamic) { + return; } - // log - console.debug('tools-form::refresh() - Recreated data structure. Refresh.'); + // finalize data + var current_state = this.tree.finalize({ + data : function(dict) { + if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { + return self.content.get({id: dict.values[0].id}).dataset_id; + } + return null; + } + }); + + // log tool state + console.debug('tools-form::_refreshForm() - Refreshing states.'); + console.debug(current_state); + + // activates/disables spinner for dynamic fields to indicate that they are currently being updated + function wait(active) { + for (var i in self.input_list) { + var field = self.field_list[i]; + var input = self.input_list[i]; + if (input.is_dynamic && field.wait && field.unwait) { + if (active) { + field.wait(); + } else { + field.unwait(); + } + } + } + } + + // set wait mode + wait(true); + + // post job + Utils.request({ + type : 'GET', + url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', + data : current_state, + success : function(response) { + // rebuild form + self._rebuildForm(response); + + // unset wait mode + wait(false); + + // log success + console.debug('tools-form::_refreshForm() - States refreshed.'); + console.debug(response); + }, + error : function(response) { + console.debug('tools-form::_refreshForm() - Refresh request failed.'); + console.debug(response); + } + }); }, // build tool model through api call @@ -123,50 +181,6 @@ }); }, - // refresh form data - rebuild: function() { - // link this - var self = this; - - // only refresh the state if the form contains dynamic parameters - if (!this.is_dynamic) { - return; - } - - // finalize data - var current_state = this.tree.finalize({ - data : function(dict) { - if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { - return self.content.get({id: dict.values[0].id}).dataset_id; - } - return null; - } - }); - - // log tool state - console.debug('tools-form::_refreshForm() - Refreshing states.'); - console.debug(current_state); - - // post job - Utils.request({ - type : 'GET', - url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', - data : current_state, - success : function(response) { - // rebuild form - self._rebuildForm(response); - - // log success - console.debug('tools-form::_refreshForm() - States refreshed.'); - console.debug(response); - }, - error : function(response) { - console.debug('tools-form::_refreshForm() - Refresh request failed.'); - console.debug(response); - } - }); - }, - // rebuild the form elements _rebuildForm: function(new_model) { var self = this; @@ -177,7 +191,7 @@ // backup new options input.options = node.options; - // get/update field (currently only done for select fields) + // get/update field var field = self.field_list[input_id]; if (field.update && input.type != 'data') { var new_options = []; @@ -296,7 +310,6 @@ cls : 'btn btn-primary', floating : 'clear', onclick : function() { - //self.rebuild(); self.job_handler.submit(); } }) @@ -328,8 +341,8 @@ // append tool section this.portlet.append(this.section.$el); - // trigger refresh - this.refresh(); + // rebuild the underlying data structure + this.rebuild(); } }); diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -6,7 +6,10 @@ // input field element wrapper return Backbone.View.extend({ // initialize input wrapper - initialize: function(options) { + initialize: function(app, options) { + // link app + this.app = app; + // link field this.field = options.field; @@ -61,10 +64,10 @@ /** Refresh element */ _refresh: function() { - // show/hide field element if (!this.field.skip) { this.$field.fadeIn('fast'); this.$title_optional.html('Disable'); + this.app.refresh(); } else { this.$field.hide(); this.$title_optional.html('Enable'); diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -142,8 +142,8 @@ if (batch_n === -1) { batch_n = n; } else { - if (batch_n !== n) { - this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); + if (batch_n !== n && n != 1) { + this._foundError(input_id, 'Please make sure that you select a single input or the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); return false; } } diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -82,7 +82,7 @@ input_def.value = input_def.test_param.value; // build options field - var table_row = this._addRow('conditional', input_def); + var field = this._addRow('conditional', input_def); // add fields for (var i in input_def.cases) { @@ -104,6 +104,9 @@ // append to table this.table.append(sub_section_id); } + + // trigger refresh on conditional input field after all input elements have been created + field.trigger('change'); }, /** Add a repeat block @@ -131,6 +134,7 @@ repeat.retitle(input_def.title); // trigger refresh + self.app.rebuild(); self.app.refresh(); } } @@ -164,6 +168,7 @@ create(input_def.inputs, true); // trigger refresh + self.app.rebuild(); self.app.refresh(); } }); @@ -187,7 +192,7 @@ } // create input field wrapper - var input_element = new InputElement({ + var input_element = new InputElement(this.app, { label : input_def.title, help : input_def.help, field : repeat @@ -297,7 +302,7 @@ this.app.field_list[id] = field; // create input field wrapper - var input_element = new InputElement({ + var input_element = new InputElement(this.app, { label : input_def.label, optional : input_def.optional, help : input_def.help, @@ -313,8 +318,8 @@ // append to table this.table.append(id); - // return table row - return this.table.get(id) + // return created field + return field; }, /** Conditional input field selector @@ -366,6 +371,9 @@ section_row.hide(); } } + + // refresh form inputs + self.app.refresh(); } }); }, @@ -378,8 +386,8 @@ id : 'field-' + input_def.id, extensions : input_def.extensions, multiple : input_def.multiple, - onchange : function(dict) { - self.app.rebuild(); + onchange : function() { + self.app.refresh(); } }); }, @@ -415,7 +423,7 @@ data : options, multiple: input_def.multiple, onchange: function() { - self.app.rebuild(); + self.app.refresh(); } }); }, diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -169,7 +169,12 @@ } } else { if (node.type == 'conditional') { - search (index, node.inputs); + var value = node.test_param && node.test_param.value; + for (var j in node.cases) { + if (node.cases[j].value == value) { + search (index, node.cases[j].inputs); + } + } } else { var input_id = self.app.tree.job_ids[index]; if (input_id) { diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -11,7 +11,8 @@ visible : true, data : [], id : Utils.uuid(), - empty : 'No data available' + errorText : 'No data available.', + waitText : 'Please wait...' }; // configure options @@ -21,11 +22,11 @@ this.setElement('<div/>'); // create elements - this.$error = $(this._templateError(options)); + this.$message = $('<div/>'); this.$options = $(this._template(options)); // append - this.$el.append(this.$error); + this.$el.append(this.$message); this.$el.append(this.$options); // hide input field @@ -121,6 +122,22 @@ return true; }, + /** Wait message during request processing + */ + wait: function() { + if (this._size() == 0) { + this._messageShow(this.options.waitText, 'info'); + this.$options.hide(); + } + }, + + /** Hide wait message + */ + unwait: function() { + this._messageHide(); + this._refresh(); + }, + /** Trigger custom onchange callback function */ _change: function() { @@ -132,13 +149,11 @@ /** Refresh options view */ _refresh: function() { - // count remaining options - var remaining = this.$el.find('.ui-option').length; - if (remaining == 0) { - this.$error.show(); + if (this._size() == 0) { + this._messageShow(this.options.errorText, 'danger'); this.$options.hide(); } else { - this.$error.hide(); + this._messageHide(); this.$options.css('display', 'inline-block'); } }, @@ -163,9 +178,26 @@ return selected.val(); } }, + + /** Returns the number of options + */ + _size: function() { + return this.$el.find('.ui-option').length; + }, - _templateError: function(options) { - return '<div class="ui-error" style="display: none;">' + options.empty + '</div>'; + /** Show message instead if options + */ + _messageShow: function(text, status) { + this.$message.show(); + this.$message.removeClass(); + this.$message.addClass('ui-message alert alert-' + status); + this.$message.html(text); + }, + + /** Hide message + */ + _messageHide: function() { + this.$message.hide(); } }); diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -107,8 +107,7 @@ /** Show the select field */ show: function() { - this.$icon.removeClass(); - this.$icon.addClass('fa fa-caret-down'); + this.unwait(); this.$select.show(); this.$el.show(); }, @@ -126,6 +125,13 @@ this.$icon.addClass('fa fa-spinner fa-spin'); }, + /** Hide spinner indicating that the request has been completed + */ + unwait: function() { + this.$icon.removeClass(); + this.$icon.addClass('fa fa-caret-down'); + }, + /** Returns true if the field is disabled */ disabled: function() { diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 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 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var 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available",visible:!0,wait:!1,multiple:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.options.multiple?(this.$select.prop("multiple",!0),this.$select.addClass("ui-select-multiple"),this.$icon.remove()):this.$el.addClass("ui-select"),this.update(this.options.data),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&this.$select.val(e),this.$select.val()},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){var t=this.$select.val();this.$select.find("option").remove();for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.$select.val(t),this.$select.val()||this.$select.val(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.precise&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()})},value:function(e){return e!==undefined&&(this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.options.onchange&&this.options.onchange(e),this.$slider&&this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),empty:"No data available"},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$error=$(this._templateError(t)),this.$options=$(this._template(t)),this.$el.append(this.$error),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){var e=this.$el.find(".ui-option").length;e==0?(this.$error.show(),this.$options.hide()):(this.$error.hide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return"null";if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_templateError:function(e){return'<div class="ui-error" style="display: none;">'+e.empty+"</div>"}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=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.find(".alert").append(t.message),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.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;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({type:"POST",url:config.root+"api/tools",data:data,success: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","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},error: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()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},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}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],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,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},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",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,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()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),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.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_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",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var 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class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - 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n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa 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o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_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",r.uuid()),this.chart.set("type","nvd3_bar"),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.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{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:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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'+e.cls+'">'+e.title+"</a></div>"}}),h=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.$el.find(".alert").append(t.message),this.$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="ui-message alert alert-'+e.status+'"/>'}}),p=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="ui-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>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},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.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;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({type:"POST",url:config.root+"api/tools",data:data,success: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","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error: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()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},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}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],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.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_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",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}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),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._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="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_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",r.uuid()),this.chart.set("type","nvd3_bar"),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.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{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 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),N.dispatch=S,N.lines=t,N.legend=i,N.xAxis=n,N.yAxis=r,N.interactiveLayer=s,d3.rebind(N,t,"defined","isArea","x","y","size","xScale","yScale","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id","interpolate"),N.options=e.utils.optionsFunc.bind(N),N.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,N):o},N.width=function(e){return arguments.length?(a=e,N):a},N.height=function(e){return arguments.length?(f=e,N):f},N.color=function(t){return 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l=d3.select(this),c=this,v=(a||parseInt(l.style("width"))||960)-u.left-u.right,N=(f||parseInt(l.style("height"))||400)-u.top-u.bottom;T.update=function(){l.call(T)},b.disabled=e.map(function(e){return!!e.disabled});if(!w){var C;w={};for(C in b)b[C]instanceof Array?w[C]=b[C].slice(0):w[C]=b[C]}if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var k=l.selectAll(".nv-noData").data([E]);return k.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),k.attr("x",u.left+v/2).attr("y",u.top+N/2).text(function(e){return e}),T}l.selectAll(".nv-noData").remove();var L=e.filter(function(e){return!e.disabled&&e.bar}),A=e.filter(function(e){return!e.bar});m=A.filter(function(e){return!e.disabled}).length&&A.filter(function(e){return!e.disabled})[0].values.length?t.xScale():n.xScale(),g=n.yScale(),y=t.yScale();var O=d3.select(this).selectAll("g.nv-wrap.nv-linePlusBar").data([e]),M=O.enter().append("g").attr("class","nvd3 nv-wrap 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D=_.select(".nv-barsWrap").datum(L.length?L:[{values:[]}]),P=_.select(".nv-linesWrap").datum(A[0]&&!A[0].disabled?A:[{values:[]}]);d3.transition(D).call(n),d3.transition(P).call(t),r.scale(m).ticks(v/100).tickSize(-N,0),_.select(".nv-x.nv-axis").attr("transform","translate(0,"+g.range()[0]+")"),d3.transition(_.select(".nv-x.nv-axis")).call(r),i.scale(g).ticks(N/36).tickSize(-v,0),d3.transition(_.select(".nv-y1.nv-axis")).style("opacity",L.length?1:0).call(i),s.scale(y).ticks(N/36).tickSize(L.length?0:-v,0),_.select(".nv-y2.nv-axis").style("opacity",A.length?1:0).attr("transform","translate("+v+",0)"),d3.transition(_.select(".nv-y2.nv-axis")).call(s),o.dispatch.on("stateChange",function(e){b=e,S.stateChange(b),T.update()}),S.on("tooltipShow",function(e){d&&x(e,c.parentNode)}),S.on("changeState",function(t){typeof t.disabled!="undefined"&&(e.forEach(function(e,n){e.disabled=t.disabled[n]}),b.disabled=t.disabled),T.update()})}),T}var t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var 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s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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job_wrapper.fail( "Unable to run this job due to a cluster error, please retry it later" ) + if not fail_msg: + fail_msg = DEFAULT_JOB_PUT_FAILURE_MESSAGE + job_wrapper.fail( fail_msg ) self.ds.deleteJobTemplate( jt ) return else: diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1124,14 +1124,18 @@ last_updated = {} for job in jobs: delta = datetime.utcnow() - job.update_time - if delta > timedelta( minutes=60 ): + if delta.days > 0: + last_updated[job.id] = '%s hours' % ( delta.days * 24 + int( delta.seconds / 60 / 60 ) ) + elif delta > timedelta( minutes=59 ): last_updated[job.id] = '%s hours' % int( delta.seconds / 60 / 60 ) else: last_updated[job.id] = '%s minutes' % int( delta.seconds / 60 ) finished = {} for job in recent_jobs: delta = datetime.utcnow() - job.update_time - if delta > timedelta( minutes=60 ): + if delta.days > 0: + finished[job.id] = '%s hours' % ( delta.days * 24 + int( delta.seconds / 60 / 60 ) ) + elif delta > timedelta( minutes=59 ): finished[job.id] = '%s hours' % int( delta.seconds / 60 / 60 ) else: finished[job.id] = '%s minutes' % int( delta.seconds / 60 ) diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 lib/galaxy/web/proxy/js/package.json --- a/lib/galaxy/web/proxy/js/package.json +++ b/lib/galaxy/web/proxy/js/package.json @@ -11,7 +11,7 @@ "url": "https://bitbucket.org/galaxy/galaxy-central" }, "dependencies": { - "http-proxy": "~1.1", + "http-proxy": "1.6.0", "commander": "~2.2", "sqlite3": "3.0.2" } diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 lib/galaxy/webapps/galaxy/api/jobs.py --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -89,6 +89,9 @@ :type id: string :param id: Specific job id + :type full: boolean + :param full: whether to return extra information + :rtype: dictionary :returns: dictionary containing full description of job data """ @@ -97,6 +100,12 @@ full_output = util.asbool( kwd.get( 'full', 'false' ) ) if full_output: job_dict.update( dict( stderr=job.stderr, stdout=job.stdout ) ) + if trans.user_is_admin(): + + def metric_to_dict(metric): + return dict(zip(['title', 'value'], trans.app.job_metrics.format(metric.plugin, metric.metric_name, metric.metric_value))) + + job_dict['job_metrics'] = [metric_to_dict(metric) for metric in job.metrics] return job_dict @expose_api @@ -248,11 +257,11 @@ ) ) for k, v in input_data.items(): - """ - Here we are attempting to link the inputs to the underlying dataset (not the dataset association) - This way, if the calulation was done using a copied HDA (copied from the library or another history) - the search will still find the job - """ + # Here we are attempting to link the inputs to the underlying + # dataset (not the dataset association). + # This way, if the calculation was done using a copied HDA + # (copied from the library or another history), the search will + # still find the job a = aliased( trans.app.model.JobToInputDatasetAssociation ) b = aliased( trans.app.model.HistoryDatasetAssociation ) query = query.filter( and_( @@ -264,9 +273,7 @@ out = [] for job in query.all(): - """ - check to make sure none of the output files have been deleted - """ + # check to make sure none of the output files have been deleted if all( list( a.dataset.deleted == False for a in job.output_datasets ) ): out.append( self.encode_all_ids( trans, job.to_dict( 'element' ), True ) ) return out diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -64,18 +64,76 @@ } }, - // refresh + // rebuild underlying data structure representation for the tool form + // this happens i.e. when repeat blocks are added or removed and on initialization + rebuild: function() { + this.tree.refresh(); + console.debug('tools-form::refresh() - Refreshed form structure.'); + }, + + // refreshes input states i.e. for dynamic parameters refresh: function() { - // recreate tree structure - this.tree.refresh(); + // link this + var self = this; - // trigger change - for (var id in this.field_list) { - this.field_list[id].trigger('change'); + // only refresh the state if the form contains dynamic parameters + if (!this.is_dynamic) { + return; } - // log - console.debug('tools-form::refresh() - Recreated data structure. Refresh.'); + // finalize data + var current_state = this.tree.finalize({ + data : function(dict) { + if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { + return self.content.get({id: dict.values[0].id}).dataset_id; + } + return null; + } + }); + + // log tool state + console.debug('tools-form::_refreshForm() - Refreshing states.'); + console.debug(current_state); + + // activates/disables spinner for dynamic fields to indicate that they are currently being updated + function wait(active) { + for (var i in self.input_list) { + var field = self.field_list[i]; + var input = self.input_list[i]; + if (input.is_dynamic && field.wait && field.unwait) { + if (active) { + field.wait(); + } else { + field.unwait(); + } + } + } + } + + // set wait mode + wait(true); + + // post job + Utils.request({ + type : 'GET', + url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', + data : current_state, + success : function(response) { + // rebuild form + self._rebuildForm(response); + + // unset wait mode + wait(false); + + // log success + console.debug('tools-form::_refreshForm() - States refreshed.'); + console.debug(response); + }, + error : function(response) { + console.debug('tools-form::_refreshForm() - Refresh request failed.'); + console.debug(response); + } + }); }, // build tool model through api call @@ -123,50 +181,6 @@ }); }, - // refresh form data - rebuild: function() { - // link this - var self = this; - - // only refresh the state if the form contains dynamic parameters - if (!this.is_dynamic) { - return; - } - - // finalize data - var current_state = this.tree.finalize({ - data : function(dict) { - if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { - return self.content.get({id: dict.values[0].id}).dataset_id; - } - return null; - } - }); - - // log tool state - console.debug('tools-form::_refreshForm() - Refreshing states.'); - console.debug(current_state); - - // post job - Utils.request({ - type : 'GET', - url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', - data : current_state, - success : function(response) { - // rebuild form - self._rebuildForm(response); - - // log success - console.debug('tools-form::_refreshForm() - States refreshed.'); - console.debug(response); - }, - error : function(response) { - console.debug('tools-form::_refreshForm() - Refresh request failed.'); - console.debug(response); - } - }); - }, - // rebuild the form elements _rebuildForm: function(new_model) { var self = this; @@ -177,7 +191,7 @@ // backup new options input.options = node.options; - // get/update field (currently only done for select fields) + // get/update field var field = self.field_list[input_id]; if (field.update && input.type != 'data') { var new_options = []; @@ -296,7 +310,6 @@ cls : 'btn btn-primary', floating : 'clear', onclick : function() { - //self.rebuild(); self.job_handler.submit(); } }) @@ -328,8 +341,8 @@ // append tool section this.portlet.append(this.section.$el); - // trigger refresh - this.refresh(); + // rebuild the underlying data structure + this.rebuild(); } }); diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -6,7 +6,10 @@ // input field element wrapper return Backbone.View.extend({ // initialize input wrapper - initialize: function(options) { + initialize: function(app, options) { + // link app + this.app = app; + // link field this.field = options.field; @@ -61,10 +64,10 @@ /** Refresh element */ _refresh: function() { - // show/hide field element if (!this.field.skip) { this.$field.fadeIn('fast'); this.$title_optional.html('Disable'); + this.app.refresh(); } else { this.$field.hide(); this.$title_optional.html('Enable'); diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -142,8 +142,8 @@ if (batch_n === -1) { batch_n = n; } else { - if (batch_n !== n) { - this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); + if (batch_n !== n && n != 1) { + this._foundError(input_id, 'Please make sure that you select a single input or the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); return false; } } diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -82,7 +82,7 @@ input_def.value = input_def.test_param.value; // build options field - var table_row = this._addRow('conditional', input_def); + var field = this._addRow('conditional', input_def); // add fields for (var i in input_def.cases) { @@ -104,6 +104,9 @@ // append to table this.table.append(sub_section_id); } + + // trigger refresh on conditional input field after all input elements have been created + field.trigger('change'); }, /** Add a repeat block @@ -131,6 +134,7 @@ repeat.retitle(input_def.title); // trigger refresh + self.app.rebuild(); self.app.refresh(); } } @@ -164,6 +168,7 @@ create(input_def.inputs, true); // trigger refresh + self.app.rebuild(); self.app.refresh(); } }); @@ -187,7 +192,7 @@ } // create input field wrapper - var input_element = new InputElement({ + var input_element = new InputElement(this.app, { label : input_def.title, help : input_def.help, field : repeat @@ -297,7 +302,7 @@ this.app.field_list[id] = field; // create input field wrapper - var input_element = new InputElement({ + var input_element = new InputElement(this.app, { label : input_def.label, optional : input_def.optional, help : input_def.help, @@ -313,8 +318,8 @@ // append to table this.table.append(id); - // return table row - return this.table.get(id) + // return created field + return field; }, /** Conditional input field selector @@ -366,6 +371,9 @@ section_row.hide(); } } + + // refresh form inputs + self.app.refresh(); } }); }, @@ -378,8 +386,8 @@ id : 'field-' + input_def.id, extensions : input_def.extensions, multiple : input_def.multiple, - onchange : function(dict) { - self.app.rebuild(); + onchange : function() { + self.app.refresh(); } }); }, @@ -415,7 +423,7 @@ data : options, multiple: input_def.multiple, onchange: function() { - self.app.rebuild(); + self.app.refresh(); } }); }, diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -169,7 +169,12 @@ } } else { if (node.type == 'conditional') { - search (index, node.inputs); + var value = node.test_param && node.test_param.value; + for (var j in node.cases) { + if (node.cases[j].value == value) { + search (index, node.cases[j].inputs); + } + } } else { var input_id = self.app.tree.job_ids[index]; if (input_id) { diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -11,7 +11,8 @@ visible : true, data : [], id : Utils.uuid(), - empty : 'No data available' + errorText : 'No data available.', + waitText : 'Please wait...' }; // configure options @@ -21,11 +22,11 @@ this.setElement('<div/>'); // create elements - this.$error = $(this._templateError(options)); + this.$message = $('<div/>'); this.$options = $(this._template(options)); // append - this.$el.append(this.$error); + this.$el.append(this.$message); this.$el.append(this.$options); // hide input field @@ -121,6 +122,22 @@ return true; }, + /** Wait message during request processing + */ + wait: function() { + if (this._size() == 0) { + this._messageShow(this.options.waitText, 'info'); + this.$options.hide(); + } + }, + + /** Hide wait message + */ + unwait: function() { + this._messageHide(); + this._refresh(); + }, + /** Trigger custom onchange callback function */ _change: function() { @@ -132,13 +149,11 @@ /** Refresh options view */ _refresh: function() { - // count remaining options - var remaining = this.$el.find('.ui-option').length; - if (remaining == 0) { - this.$error.show(); + if (this._size() == 0) { + this._messageShow(this.options.errorText, 'danger'); this.$options.hide(); } else { - this.$error.hide(); + this._messageHide(); this.$options.css('display', 'inline-block'); } }, @@ -163,9 +178,26 @@ return selected.val(); } }, + + /** Returns the number of options + */ + _size: function() { + return this.$el.find('.ui-option').length; + }, - _templateError: function(options) { - return '<div class="ui-error" style="display: none;">' + options.empty + '</div>'; + /** Show message instead if options + */ + _messageShow: function(text, status) { + this.$message.show(); + this.$message.removeClass(); + this.$message.addClass('ui-message alert alert-' + status); + this.$message.html(text); + }, + + /** Hide message + */ + _messageHide: function() { + this.$message.hide(); } }); diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -107,8 +107,7 @@ /** Show the select field */ show: function() { - this.$icon.removeClass(); - this.$icon.addClass('fa fa-caret-down'); + this.unwait(); this.$select.show(); this.$el.show(); }, @@ -126,6 +125,13 @@ this.$icon.addClass('fa fa-spinner fa-spin'); }, + /** Hide spinner indicating that the request has been completed + */ + unwait: function() { + this.$icon.removeClass(); + this.$icon.addClass('fa fa-caret-down'); + }, + /** Returns true if the field is disabled */ disabled: function() { diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},rebuild:function(){var m=this;if(!this.is_dynamic){return}var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){m._rebuildForm(o);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type!="data"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::refresh() - Refreshed form structure.")},refresh:function(){var m=this;if(!this.is_dynamic){return}var n=this.tree.finalize({data:function(p){if(p.values.length>0&&p.values[0]&&p.values[0].src==="hda"){return m.content.get({id:p.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(n);function o(s){for(var q in m.input_list){var r=m.field_list[q];var p=m.input_list[q];if(p.is_dynamic&&r.wait&&r.unwait){if(s){r.wait()}else{r.unwait()}}}}o(true);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(p){m._rebuildForm(p);o(false);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(p)},error:function(p){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(p)}})},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type!="data"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch();this.$el.append(p.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(b){this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(c,b){this.app=c;this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable");this.app.refresh()}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(j&&e&&e.validate&&!e.validate()){this._foundError(l);return false}if(f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(j&&e&&e.validate&&!e.validate()){this._foundError(l);return false}if(f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g&&g!=1){this._foundError(l,"Please make sure that you select a single input or the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(j){i.app.rebuild()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.rebuild()}})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var l=this._addRow("conditional",h);for(var k in h.cases){var j=h.id+"-section-"+k;var m=new f(this.app,{inputs:h.cases[k].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(j)}l.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return i},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}j.app.refresh()}})},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(k,n){for(var h in n){var f=n[h];if(f.input){var p=f.input;var j=k;if(k!=""){j+="|"}j+=p.name;switch(p.type){case"repeat":var e="section-";var s=[];var m=null;for(var r in f){var l=r.indexOf(e);if(l!=-1){l+=e.length;s.push(parseInt(r.substr(l)));if(!m){m=r.substr(0,l)}}}s.sort(function(t,i){return t-i});var h=0;for(var g in s){b(j+"_"+h++,f[m+s[g]])}break;case"conditional":var q=a.app.field_list[p.id].value();c(j+"|"+p.test_param.name,p.id,q);for(var g in p.cases){if(p.cases[g].value==q){b(j,n[p.id+"-section-"+g]);break}}break;default:var o=a.app.field_list[p.id];var q=o.value();if(d[p.type]){q=d[p.type](q)}if(!o.skip){c(j,p.id,q)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchModel:function(c,e){var a={};var b=this;function d(n,l){for(var k in l){var m=l[k];var h=m.name;if(n!=""){h=n+"|"+h}if(m.type=="repeat"){for(var g in m.cache){d(h+"_"+g,m.cache[g])}}else{if(m.type=="conditional"){d(h,m.inputs)}else{var f=b.app.tree.job_ids[h];if(f){e(f,m)}}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(k,n){for(var h in n){var f=n[h];if(f.input){var p=f.input;var j=k;if(k!=""){j+="|"}j+=p.name;switch(p.type){case"repeat":var e="section-";var s=[];var m=null;for(var r in f){var l=r.indexOf(e);if(l!=-1){l+=e.length;s.push(parseInt(r.substr(l)));if(!m){m=r.substr(0,l)}}}s.sort(function(t,i){return t-i});var h=0;for(var g in s){b(j+"_"+h++,f[m+s[g]])}break;case"conditional":var q=a.app.field_list[p.id].value();c(j+"|"+p.test_param.name,p.id,q);for(var g in p.cases){if(p.cases[g].value==q){b(j,n[p.id+"-section-"+g]);break}}break;default:var o=a.app.field_list[p.id];var q=o.value();if(d[p.type]){q=d[p.type](q)}if(!o.skip){c(j,p.id,q)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchModel:function(c,e){var a={};var b=this;function d(o,l){for(var k in l){var m=l[k];var h=m.name;if(o!=""){h=o+"|"+h}if(m.type=="repeat"){for(var g in m.cache){d(h+"_"+g,m.cache[g])}}else{if(m.type=="conditional"){var n=m.test_param&&m.test_param.value;for(var g in m.cases){if(m.cases[g].value==n){d(h,m.cases[g].inputs)}}}else{var f=b.app.tree.job_ids[h];if(f){e(f,m)}}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$error=$(this._templateError(g));this.$options=$(this._template(g));this.$el.append(this.$error);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){var f=this.$el.find(".ui-option").length;if(f==0){this.$error.show();this.$options.hide()}else{this.$error.hide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_templateError:function(f){return'<div class="ui-error" style="display: none;">'+f.empty+"</div>"}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1292,7 +1292,7 @@ .ui-table-form-info{clear:both !important} .ui-table-form-separator{font-weight:bold;font-size:0.9em} .ui-label{font-weight:bold} -.ui-message{padding:2px 2px 2px 10px} +.ui-message{padding:2px 2px 2px 10px;margin-bottom:5px} .ui-icon{font-size:1.2em} .ui-button-icon{margin-right:5px}.ui-button-icon ul i{font-size:1.2em;margin-right:5px;position:relative;top:1px} .ui-button-icon .button{margin-right:5px;margin-left:5px}.ui-button-icon .button .title{position:relative;font-size:0.8em;font-weight:normal;top:-1px} diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -81,6 +81,7 @@ .ui-message { padding: 2px 2px 2px 10px; + margin-bottom: 5px; } .ui-icon { diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 tools/filters/convert_characters.py --- a/tools/filters/convert_characters.py +++ b/tools/filters/convert_characters.py @@ -1,30 +1,18 @@ #!/usr/bin/env python #By, Guruprasad Ananda. +import optparse import re -import sys - -def stop_err(msg): - sys.stderr.write(msg) - sys.exit() - - -def main(): - if len(sys.argv) != 4: - stop_err("usage: convert_characters infile from_char outfile") - - try: - fin = open(sys.argv[1], 'r') - except: - stop_err("Input file cannot be opened for reading.") - - from_char = sys.argv[2] - - try: - fout = open(sys.argv[3], 'w') - except: - stop_err("Output file cannot be opened for writing.") +def __main__(): + parser = optparse.OptionParser() + parser.add_option('--strip', action='store_true', + help='strip leading and trailing whitespaces') + parser.add_option('--condense', action='store_true', + help='condense consecutive delimiters') + (options, args) = parser.parse_args() + if len(args) != 3: + parser.error("usage: convert_characters.py infile from_char outfile") char_dict = { 'T': '\t', @@ -38,20 +26,26 @@ 'Sc': ';' } # regexp to match 1 or more occurences. - from_ch = char_dict[from_char] + '+' + from_char = args[1] + from_ch = char_dict[from_char] + if options.condense: + from_ch += '+' + skipped = 0 + with open(args[0], 'rU') as fin: + with open(args[2], 'w') as fout: + for line in fin: + if options.strip: + line = line.strip() + else: + line = line.rstrip('\n') + try: + fout.write("%s\n" % (re.sub(from_ch, '\t', line))) + except: + skipped += 1 - for line in fin: - line = line.strip() - try: - fout.write("%s\n" % (re.sub(from_ch, '\t', line))) - except: - skipped += 1 - - fin.close() - fout.close() if skipped: print "Skipped %d lines as invalid." % skipped if __name__ == "__main__": - main() + __main__() diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 tools/filters/convert_characters.xml --- a/tools/filters/convert_characters.xml +++ b/tools/filters/convert_characters.xml @@ -1,59 +1,77 @@ -<tool id="Convert characters1" name="Convert"> - <description>delimiters to TAB</description> - <command interpreter="python">convert_characters.py $input $convert_from $out_file1</command> - <inputs> - <param name="convert_from" type="select" label="Convert all"> - <option value="s">Whitespaces</option> - <option value="T">Tabs</option> -  - <option value="Dt">Dots</option> - <option value="C">Commas</option> - <option value="D">Dashes</option> - <option value="U">Underscores</option> - <option value="P">Pipes</option> - <option value="Co">Colons</option> - <option value="Sc">Semicolons</option> - </param> - <param format="txt" name="input" type="data" label="in Dataset"/> - </inputs> - <outputs> - <data format="tabular" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="convert_from" value="s"/> - <param name="input" value="1.bed"/> - <output name="out_file1" file="eq-convert.dat"/> - </test> - <test> - <param name="convert_from" value="s"/> - <param name="input" value="a.txt"/> - <output name="out_file1" file="a.tab"/> - </test> - </tests> - <help> - -**What it does** - -Converts all delimiters of a specified type into TABs. Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab. - ------ - -**Example** - -- Input file:: - - chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|- - chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|- - chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+ - chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+ - -- Converting all pipe delimiters of the above file to TABs will get:: - - chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 - - chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 - - chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 + - chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 + - -</help> -</tool> +<tool id="Convert characters1" name="Convert"> + <description>delimiters to TAB</description> + <command interpreter="python"> +convert_characters.py +#if $strip + --strip +#end if +#if $condense + --condense +#end if +$input $convert_from $out_file1 + </command> + <inputs> + <param name="convert_from" type="select" label="Convert all"> + <option value="s">Whitespaces</option> + <option value="T">Tabs</option> +  + <option value="Dt">Dots</option> + <option value="C">Commas</option> + <option value="D">Dashes</option> + <option value="U">Underscores</option> + <option value="P">Pipes</option> + <option value="Co">Colons</option> + <option value="Sc">Semicolons</option> + </param> + <param format="txt" name="input" type="data" label="in Dataset"/> + <param name="strip" type="boolean" checked="true" label="Strip leading and trailing whitespaces" /> + <param name="condense" type="boolean" checked="true" label="Condense consecutive delimiters in one TAB" /> + </inputs> + <outputs> + <data format="tabular" name="out_file1" /> + </outputs> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <tests> + <test> + <param name="convert_from" value="s"/> + <param name="input" value="1.bed"/> + <param name="strip" value="true" /> + <param name="condense" value="true" /> + <output name="out_file1" file="eq-convert.dat"/> + </test> + <test> + <param name="convert_from" value="s"/> + <param name="input" value="a.txt"/> + <param name="strip" value="true" /> + <param name="condense" value="true" /> + <output name="out_file1" file="a.tab"/> + </test> + </tests> + <help> + +**What it does** + +Converts all delimiters of a specified type into TABs. Consecutive delimiters can be condensed in a single TAB. + +----- + +**Example** + +- Input file:: + + chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|- + chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|- + chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+ + chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+ + +- Converting all pipe delimiters of the above file to TABs and condensing delimiters will get:: + + chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 - + chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 - + chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 + + chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 + + + </help> +</tool> diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 tools/sr_assembly/velvetg.xml --- a/tools/sr_assembly/velvetg.xml +++ b/tools/sr_assembly/velvetg.xml @@ -4,7 +4,6 @@ <command interpreter="python"> velvetg_wrapper.py '$input.extra_files_path' - '$contigs' '$stats' '$LastGraph' '$velvet_asm' '$unused_reads_fasta' #if $generate_amos.afg == "yes": -amos_file $generate_amos.afg #end if @@ -96,7 +95,7 @@ <when value="yes"/></conditional> - <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="track short read positions" help=" tracking of short read positions in assembly"/> + <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" /><conditional name="coverage"><param name="cutoff" type="select" label="Coverage cutoff" help=""> @@ -169,20 +168,20 @@ </conditional></inputs><outputs> -  - <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph"> + <data format="txt" name="Graph2" label="${tool.name} on ${on_string}: Graph2" from_work_dir="Graph2"> + <filter>read_trkg is True</filter> + </data> + <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph" from_work_dir="LastGraph"><filter>last_graph['generate_graph'] == "yes"</filter></data> - <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg"> + <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg" from_work_dir="velvet_asm.afg"><filter>generate_amos['afg'] == "yes"</filter></data> - <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads"> + <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads" from_work_dir="UnusedReads.fa"><filter>unused_reads['generate_unused'] == "yes"</filter></data> - <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats"/> - <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs"/> + <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" /> + <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" /></outputs><requirements><requirement type="package">velvet</requirement> diff -r 6e6867f885b36321be98635c50c2279fc88c8fd0 -r 09e676cbd155158ddcbc4fd134f4768827df45a5 tools/sr_assembly/velvetg_wrapper.py --- a/tools/sr_assembly/velvetg_wrapper.py +++ b/tools/sr_assembly/velvetg_wrapper.py @@ -4,14 +4,9 @@ Classes encapsulating decypher tool. James E Johnson - University of Minnesota """ -import pkg_resources; -import logging, os, string, sys, tempfile, glob, shutil, types, urllib -import shlex, subprocess -from optparse import OptionParser, OptionGroup -from stat import * - - -log = logging.getLogger( __name__ ) +import os +import sys +import subprocess assert sys.version_info[:2] >= ( 2, 4 ) @@ -19,20 +14,15 @@ sys.stderr.write( "%s\n" % msg ) sys.exit() + def __main__(): #Parse Command Line - s = 'velvetg_wrapper.py: argv = %s\n' % (sys.argv) - # print >> sys.stderr, s # so will appear as blurb for file - argcnt = len(sys.argv) working_dir = sys.argv[1] - contigs = sys.argv[2] - stats = sys.argv[3] - LastGraph = sys.argv[4] - afgFile = sys.argv[5] - unusedReadsFile = sys.argv[6] - inputs = string.join(sys.argv[7:],' ') - cmdline = 'velvetg %s %s > /dev/null' % (working_dir, inputs) - # print >> sys.stderr, cmdline # so will appear as blurb for file + inputs = ' '.join(sys.argv[2:]) + for _ in ('Roadmaps', 'Sequences'): + os.symlink(os.path.join(working_dir, _), _) + cmdline = 'velvetg . %s' % (inputs) + print "Command to be executed: %s" % cmdline try: proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) returncode = proc.wait() @@ -50,41 +40,7 @@ raise Exception, stderr except Exception, e: stop_err( 'Error running velvetg ' + str( e ) ) - out = open(contigs,'w') - contigs_path = os.path.join(working_dir,'contigs.fa') - for line in open( contigs_path ): - out.write( "%s" % (line) ) - out.close() - out = open(stats,'w') - stats_path = os.path.join(working_dir,'stats.txt') - for line in open( stats_path ): - out.write( "%s" % (line) ) - out.close() - if LastGraph != 'None': - out = open(LastGraph,'w') - LastGraph_path = os.path.join(working_dir,'LastGraph') - for line in open( LastGraph_path ): - out.write( "%s" % (line) ) - out.close() - if afgFile != 'None': - out = open(afgFile,'w') - afgFile_path = os.path.join(working_dir,'velvet_asm.afg') - try: - for line in open( afgFile_path ): - out.write( "%s" % (line) ) - except: - logging.warn( 'error reading %s' %(afgFile_path)) - pass - out.close() - if unusedReadsFile != 'None': - out = open(unusedReadsFile,'w') - unusedReadsFile_path = os.path.join(working_dir,'UnusedReads.fa') - try: - for line in open( unusedReadsFile_path ): - out.write( "%s" % (line) ) - except: - logging.info( 'error reading %s' %(unusedReadsFile_path)) - pass - out.close() -if __name__ == "__main__": __main__() + +if __name__ == "__main__": + __main__() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Handle all submission failures in the drmaa runner.
by commits-noreply＠bitbucket.org 03 Nov '14

03 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1bb61cbf8082/ Changeset: 1bb61cbf8082 User: natefoo Date: 2014-11-03 18:58:14+00:00 Summary: Handle all submission failures in the drmaa runner. Affected #: 1 file diff -r 25ea95428c508c7982a3f9ff2af855eac7c62dbb -r 1bb61cbf80825b0793a61d83f01925b57467d3a9 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -13,6 +13,7 @@ from galaxy import eggs from galaxy import model from galaxy.jobs import JobDestination +from galaxy.jobs.handler import DEFAULT_JOB_PUT_FAILURE_MESSAGE from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner eggs.require( "drmaa" ) @@ -170,6 +171,7 @@ # TODO: configurable max tries and sleep trynum = 0 external_job_id = None + fail_msg = None while external_job_id is None and trynum < 5: try: external_job_id = self.ds.runJob(jt) @@ -177,10 +179,16 @@ except ( drmaa.InternalException, drmaa.DeniedByDrmException ), e: trynum += 1 log.warning( '(%s) drmaa.Session.runJob() failed, will retry: %s', galaxy_id_tag, e ) + fail_msg = "Unable to run this job due to a cluster error, please retry it later" time.sleep( 5 ) + except: + log.exception( '(%s) drmaa.Session.runJob() failed unconditionally', galaxy_id_tag ) + trynum = 5 else: log.error( "(%s) All attempts to submit job failed" % galaxy_id_tag ) - job_wrapper.fail( "Unable to run this job due to a cluster error, please retry it later" ) + if not fail_msg: + fail_msg = DEFAULT_JOB_PUT_FAILURE_MESSAGE + job_wrapper.fail( fail_msg ) self.ds.deleteJobTemplate( jt ) return else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: nsoranzo: API: Return also metrics for jobs when full=True and user is admin.
by commits-noreply＠bitbucket.org 02 Nov '14

02 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/25ea95428c50/ Changeset: 25ea95428c50 User: nsoranzo Date: 2014-10-31 16:16:20+00:00 Summary: API: Return also metrics for jobs when full=True and user is admin. Affected #: 1 file diff -r bd2ec092d2f57aa8526b7d6612403b7ae4354907 -r 25ea95428c508c7982a3f9ff2af855eac7c62dbb lib/galaxy/webapps/galaxy/api/jobs.py --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -89,6 +89,9 @@ :type id: string :param id: Specific job id + :type full: boolean + :param full: whether to return extra information + :rtype: dictionary :returns: dictionary containing full description of job data """ @@ -97,6 +100,12 @@ full_output = util.asbool( kwd.get( 'full', 'false' ) ) if full_output: job_dict.update( dict( stderr=job.stderr, stdout=job.stdout ) ) + if trans.user_is_admin(): + + def metric_to_dict(metric): + return dict(zip(['title', 'value'], trans.app.job_metrics.format(metric.plugin, metric.metric_name, metric.metric_value))) + + job_dict['job_metrics'] = [metric_to_dict(metric) for metric in job.metrics] return job_dict @expose_api @@ -248,11 +257,11 @@ ) ) for k, v in input_data.items(): - """ - Here we are attempting to link the inputs to the underlying dataset (not the dataset association) - This way, if the calulation was done using a copied HDA (copied from the library or another history) - the search will still find the job - """ + # Here we are attempting to link the inputs to the underlying + # dataset (not the dataset association). + # This way, if the calculation was done using a copied HDA + # (copied from the library or another history), the search will + # still find the job a = aliased( trans.app.model.JobToInputDatasetAssociation ) b = aliased( trans.app.model.HistoryDatasetAssociation ) query = query.filter( and_( @@ -264,9 +273,7 @@ out = [] for job in query.all(): - """ - check to make sure none of the output files have been deleted - """ + # check to make sure none of the output files have been deleted if all( list( a.dataset.deleted == False for a in job.output_datasets ) ): out.append( self.encode_all_ids( trans, job.to_dict( 'element' ), True ) ) return out Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Another fix like PR 546.
by commits-noreply＠bitbucket.org 02 Nov '14

02 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bd2ec092d2f5/ Changeset: bd2ec092d2f5 User: jmchilton Date: 2014-11-02 21:17:26+00:00 Summary: Another fix like PR 546. Affected #: 1 file diff -r 51f4c1c7fce753eb28ec907715d324a2bca2c84a -r bd2ec092d2f57aa8526b7d6612403b7ae4354907 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1133,7 +1133,9 @@ finished = {} for job in recent_jobs: delta = datetime.utcnow() - job.update_time - if delta > timedelta( minutes=60 ): + if delta.days > 0: + finished[job.id] = '%s hours' % ( delta.days * 24 + int( delta.seconds / 60 / 60 ) ) + elif delta > timedelta( minutes=59 ): finished[job.id] = '%s hours' % int( delta.seconds / 60 / 60 ) else: finished[job.id] = '%s minutes' % int( delta.seconds / 60 ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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