From 417d1d251e7e7c735a8d4aefd53edcec941db1f4 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 14 Mar 2017 13:59:57 -0400 Subject: [PATCH 01/14] Initial commit to get this rolling, library-security does not exist and needs to be created, among others. --- CITATION | 2 +- client/galaxy/scripts/mvc/citation/citation-view.js | 2 +- client/galaxy/scripts/mvc/library/library-folderlist-view.js | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CITATION b/CITATION index 1e6092ee725..b279bf3eba2 100644 --- a/CITATION +++ b/CITATION @@ -16,7 +16,7 @@ following publications: a platform for interactive large-scale genome analysis." Genome Research. 2005 Oct; 15(10):1451-5. -See also: http://wiki.galaxyproject.org/CitingGalaxy +See also: http://galaxyproject.org/citing-galaxy diff --git a/client/galaxy/scripts/mvc/citation/citation-view.js b/client/galaxy/scripts/mvc/citation/citation-view.js index 5fb36002468..baccd25a9d7 100644 --- a/client/galaxy/scripts/mvc/citation/citation-view.js +++ b/client/galaxy/scripts/mvc/citation/citation-view.js @@ -151,7 +151,7 @@ var CitationListView = Backbone.View.extend({ ' citations explicitly at this time. When writing up your analysis, please manually', ' review your histories and find all references', ' that should be cited in order to completely describe your work. Also, please remember to', - ' cite Galaxy.', + ' cite Galaxy.', '', ].join(''); } else { diff --git a/client/galaxy/scripts/mvc/library/library-folderlist-view.js b/client/galaxy/scripts/mvc/library/library-folderlist-view.js index 5221125b371..33d803edccc 100644 --- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js +++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js @@ -386,7 +386,7 @@ var FolderListView = Backbone.View.extend({ '', '' ].join('')); From bc870cdf66ecaaf218cd20debdbcc68b20e7f959 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 14 Mar 2017 14:19:01 -0400 Subject: [PATCH 02/14] Update galaxy.ini.sample and config. --- config/galaxy.ini.sample | 40 +++++++++++++++++++++------------------- lib/galaxy/config.py | 4 ++-- 2 files changed, 23 insertions(+), 21 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 15f849cd585..be2cecc8f22 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -11,9 +11,10 @@ # values are set to the default value. Relative paths are relative to the root # Galaxy directory. # -# Examples of many of these options are explained in more detail in the wiki: +# Examples of many of these options are explained in more detail in the Galaxy +# Community Hub. # -# https://wiki.galaxyproject.org/Admin/Config +# https://galaxyproject.org/admin/config # # Config hackers are encouraged to check there before asking for help. @@ -179,7 +180,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory # Path to the directory in which tool dependencies are placed. This is used by # the Tool Shed to install dependencies and can also be used by administrators # to manually install or link to dependencies. For details, see: -# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies +# https://galaxyproject.org/admin/config/tool-dependencies # Set the string to None to explicitly disable tool dependency handling. # If this option is set to none or an invalid path, installing tools with dependencies # from the Tool Shed will fail. @@ -305,9 +306,9 @@ paste.app_factory = galaxy.web.buildapp:app_factory # applied to the ToolDataTableManager at server start up. #shed_tool_data_table_config = config/shed_tool_data_table_conf.xml -# Directory where data used by tools is located, see the samples in that -# directory and the wiki for help: -# https://wiki.galaxyproject.org/Admin/DataIntegration +# Directory where data used by tools is located. See the samples in that +# directory and the Galaxy Community Hub for help: +# https://galaxyproject.org/admin/data-integration #tool_data_path = tool-data # Directory where Tool Data Table related files will be placed @@ -478,7 +479,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory # URL of the support resource for the galaxy instance. Used in activation # emails. -#instance_resource_url = https://wiki.galaxyproject.org/ +#instance_resource_url = https://galaxyproject.org/ # E-mail domains blacklist is used for filtering out users that are using # disposable email address during the registration. If their address domain @@ -539,7 +540,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory # bypass security to display datasets. Please be aware that there are security # implications if this is allowed. More details (including required changes to # the proxy server config) are available in the Apache proxy documentation on -# the wiki. +# the Galaxy Community Hub. # # The list of servers in this sample config are for the UCSC Main, Test and # Archaea browsers, but the default if left commented is to not allow any @@ -605,19 +606,19 @@ nglims_config_file = tool-data/nglims.yaml #logo_url = / # The URL linked by the "Wiki" link in the "Help" menu. -#wiki_url = https://wiki.galaxyproject.org/ +#wiki_url = https://galaxyproject.org/ # The URL linked by the "Support" link in the "Help" menu. -#support_url = https://wiki.galaxyproject.org/Support +#support_url = https://galaxyproject.org/support # The URL linked by the "How to Cite Galaxy" link in the "Help" menu. -#citation_url = https://wiki.galaxyproject.org/CitingGalaxy +#citation_url = https://galaxyproject.org/citing-galaxy # The URL linked by the "Search" link in the "Help" menu. -#search_url = http://galaxyproject.org/search/usegalaxy/ +#search_url = http://galaxyproject.org/search/ # The URL linked by the "Mailing Lists" link in the "Help" menu. -#mailing_lists_url = https://wiki.galaxyproject.org/MailingLists +#mailing_lists_url = https://galaxyproject.org/mailing-lists # The URL linked by the "Videos" link in the "Help" menu. #screencasts_url = https://vimeo.com/galaxyproject @@ -872,8 +873,9 @@ use_interactive = True # -- Data Libraries -# These library upload options are described in much more detail in the wiki: -# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles +# These library upload options are described in much more detail in the Galaxy +# Community Hub: +# https://galaxyproject.org/admin/data-libraries/uploading-library-files # Add an option to the library upload form which allows administrators to # upload a directory of files. @@ -959,7 +961,7 @@ use_interactive = True # User authentication can be delegated to an upstream proxy server (usually # Apache). The upstream proxy should set a REMOTE_USER header in the request. # Enabling remote user disables regular logins. For more information, see: -# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy +# https://galaxyproject.org/admin/config/apache-proxy #use_remote_user = False # If use_remote_user is enabled and your external authentication @@ -1002,7 +1004,7 @@ use_interactive = True # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: -# https://wiki.galaxyproject.org/Admin/Interface +# https://galaxyproject.org/admin/interface #admin_users = None # Force everyone to log in (disable anonymous access). @@ -1181,7 +1183,7 @@ use_interactive = True # separate Galaxy into multiple processes. There are more than one way to do # this, and they are explained in detail in the documentation: # -# https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling +# https://galaxyproject.org/admin/config/performance/scaling # By default, Galaxy manages and executes jobs from within a single process and # notifies itself of new jobs via in-memory queues. Jobs are run locally on @@ -1270,7 +1272,7 @@ use_interactive = True # actual user instead of as the user running the Galaxy server process. For # details on these options, see the documentation at: # -# https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster +# https://galaxyproject.org/admin/config/performance/cluster # #drmaa_external_runjob_script = scripts/drmaa_external_runner.py #drmaa_external_killjob_script = scripts/drmaa_external_killer.py diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index fd6e11a3117..ff3e7453539 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -363,8 +363,8 @@ class Configuration( object ): self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) ) self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) - self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' ) - self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) + self.support_url = kwargs.get( 'support_url', 'https://galaxyproject.org/support' ) + self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.library_import_dir = kwargs.get( 'library_import_dir', None ) From 11829c4f9df12cf8e8e3e7a14dc11e9a02afe6a4 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 14 Mar 2017 14:30:02 -0400 Subject: [PATCH 03/14] More defaults, these should be consolidated. --- lib/galaxy/managers/configuration.py | 6 +++--- templates/webapps/galaxy/galaxy.masthead.mako | 10 +++++----- templates/webapps/tool_shed/base_panels.mako | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py index 805c3958df5..e79f84ff885 100644 --- a/lib/galaxy/managers/configuration.py +++ b/lib/galaxy/managers/configuration.py @@ -44,10 +44,10 @@ class ConfigSerializer( base.ModelSerializer ): # TODO: don't hardcode here - hardcode defaults once in config.py 'wiki_url' : _defaults_to( "http://galaxyproject.org/" ), 'search_url' : _defaults_to( "http://galaxyproject.org/search/usegalaxy/" ), - 'mailing_lists' : _defaults_to( "https://wiki.galaxyproject.org/MailingLists" ), + 'mailing_lists' : _defaults_to( "https://galaxyproject.org/mailing-lists" ), 'screencasts_url' : _defaults_to( "https://vimeo.com/galaxyproject" ), - 'citation_url' : _defaults_to( "https://wiki.galaxyproject.org/CitingGalaxy" ), - 'support_url' : _defaults_to( "https://wiki.galaxyproject.org/Support" ), + 'citation_url' : _defaults_to( "https://galaxyproject.org/citing-galaxy" ), + 'support_url' : _defaults_to( "https://galaxyproject.org/support" ), 'lims_doc_url' : _defaults_to( "https://usegalaxy.org/u/rkchak/p/sts" ), 'biostar_url' : _defaults_to( '' ), 'biostar_url_redirect' : lambda *a, **c: self.url_for( controller='biostar', action='biostar_redirect', qualified=True ), diff --git a/templates/webapps/galaxy/galaxy.masthead.mako b/templates/webapps/galaxy/galaxy.masthead.mako index 2bdbd904304..f5ee61bc152 100644 --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -15,12 +15,12 @@ 'lims_doc_url' : app.config.get("lims_doc_url", "https://usegalaxy.org/u/rkchak/p/sts"), 'biostar_url' : app.config.biostar_url, 'biostar_url_redirect' : h.url_for( controller='biostar', action='biostar_redirect', qualified=True ), - 'support_url' : app.config.get("support_url", "https://wiki.galaxyproject.org/Support"), + 'support_url' : app.config.get("support_url", "https://galaxyproject.org/support"), 'search_url' : app.config.get("search_url", "http://galaxyproject.org/search/usegalaxy/"), - 'mailing_lists' : app.config.get("mailing_lists", "https://wiki.galaxyproject.org/MailingLists"), + 'mailing_lists' : app.config.get("mailing_lists", "https://galaxyproject.org/mailing-lists"), 'screencasts_url' : app.config.get("screencasts_url", "https://vimeo.com/galaxyproject"), - 'wiki_url' : app.config.get("wiki_url", "https://wiki.galaxyproject.org/"), - 'citation_url' : app.config.get("citation_url", "https://wiki.galaxyproject.org/CitingGalaxy"), + 'wiki_url' : app.config.get("wiki_url", "https://galaxyproject.org/"), + 'citation_url' : app.config.get("citation_url", "https://galaxyproject.org/citing-galaxy"), 'terms_url' : app.config.get("terms_url", ""), 'allow_user_creation' : app.config.allow_user_creation, 'logo_url' : h.url_for(app.config.get( 'logo_url', '/')), @@ -78,4 +78,4 @@ }); }); - \ No newline at end of file + diff --git a/templates/webapps/tool_shed/base_panels.mako b/templates/webapps/tool_shed/base_panels.mako index 8bfcde8b403..f735814f634 100644 --- a/templates/webapps/tool_shed/base_panels.mako +++ b/templates/webapps/tool_shed/base_panels.mako @@ -115,13 +115,13 @@ if qa_url: menu_options = [ [_('Galaxy Q&A'), qa_url, "_blank" ] ] menu_options.extend( [ - [_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://wiki.galaxyproject.org/ToolShed" ), "_blank" ], - [_('Support'), app.config.get( "support_url", "https://wiki.galaxyproject.org/Support" ), "_blank" ], + [_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://galaxyproject.org/tool-shed" ), "_blank" ], + [_('Support'), app.config.get( "support_url", "https://galaxyproject.org/support" ), "_blank" ], [_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/usegalaxy/" ), "_blank" ], - [_('Mailing Lists'), app.config.get( "mailing_lists_url", "https://wiki.galaxyproject.org/MailingLists" ), "_blank" ], + [_('Mailing Lists'), app.config.get( "mailing_lists_url", "https://galaxyproject.org/mailing-lists" ), "_blank" ], [_('Videos'), app.config.get( "screencasts_url", "https://vimeo.com/galaxyproject" ), "_blank" ], [_('Wiki'), app.config.get( "wiki_url", "http://galaxyproject.org/" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "https://wiki.galaxyproject.org/CitingGalaxy" ), "_blank" ] + [_('How to Cite Galaxy'), app.config.get( "citation_url", "https://galaxyproject.org/citing-galaxy" ), "_blank" ] ] ) tab( "help", _("Help"), None, menu_options=menu_options ) %> From e12c07cacd12fbf4a2fb148242be5bea7c13221e Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 14 Mar 2017 14:55:58 -0400 Subject: [PATCH 04/14] Use config.py for defaults used in managers/configuration. --- lib/galaxy/config.py | 1 + lib/galaxy/managers/configuration.py | 11 +++++------ .../select_shed_tool_panel_config.mako | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index ff3e7453539..4e59e6f64bd 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -364,6 +364,7 @@ class Configuration( object ): self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) self.support_url = kwargs.get( 'support_url', 'https://galaxyproject.org/support' ) + self.citation_url = kwargs.get( 'citation_url', 'https://galaxyproject.org/citing-galaxy' ) self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py index e79f84ff885..fc34afdd619 100644 --- a/lib/galaxy/managers/configuration.py +++ b/lib/galaxy/managers/configuration.py @@ -41,13 +41,12 @@ class ConfigSerializer( base.ModelSerializer ): 'logo_src' : lambda i, k, **c: self.url_for( '/static/images/galaxyIcon_noText.png' ), 'terms_url' : _defaults_to( '' ), - # TODO: don't hardcode here - hardcode defaults once in config.py - 'wiki_url' : _defaults_to( "http://galaxyproject.org/" ), - 'search_url' : _defaults_to( "http://galaxyproject.org/search/usegalaxy/" ), - 'mailing_lists' : _defaults_to( "https://galaxyproject.org/mailing-lists" ), + 'wiki_url' : _defaults_to( self.app.config.wiki_url ), + 'search_url' : _defaults_to( self.app.config.wiki_url.rstrip("/") + "/search/" ), + 'mailing_lists' : _defaults_to( self.app.config.wiki_url.rstrip("/") + "/mailing-lists/"), 'screencasts_url' : _defaults_to( "https://vimeo.com/galaxyproject" ), - 'citation_url' : _defaults_to( "https://galaxyproject.org/citing-galaxy" ), - 'support_url' : _defaults_to( "https://galaxyproject.org/support" ), + 'citation_url' : _defaults_to( self.app.config.citation_url ), + 'support_url' : _defaults_to( self.app.config.support_url ), 'lims_doc_url' : _defaults_to( "https://usegalaxy.org/u/rkchak/p/sts" ), 'biostar_url' : _defaults_to( '' ), 'biostar_url_redirect' : lambda *a, **c: self.url_for( controller='biostar', action='biostar_redirect', qualified=True ), diff --git a/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako index efec7aee1b9..f5a5cf21fe5 100644 --- a/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako +++ b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako @@ -52,7 +52,7 @@ repository tools may include code that produces malicious behavior, so be aware of what you are installing.

- If you discover a repository that causes problems after installation, contact Galaxy support, + If you discover a repository that causes problems after installation, contact Galaxy support, sending all necessary information, and appropriate action will be taken.

From ed1d19a967989416caebd3588fe6b8b6460764e2 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 14 Mar 2017 15:46:38 -0400 Subject: [PATCH 05/14] Update reports and toolshed app configs as well. --- lib/galaxy/webapps/reports/config.py | 2 +- lib/galaxy/webapps/tool_shed/config.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/webapps/reports/config.py b/lib/galaxy/webapps/reports/config.py index a56168425be..89289aa78e8 100644 --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -45,7 +45,7 @@ class Configuration( object ): self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) ) self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) - self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) + self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False diff --git a/lib/galaxy/webapps/tool_shed/config.py b/lib/galaxy/webapps/tool_shed/config.py index d787ace36c6..2526e8dfa81 100644 --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -113,8 +113,8 @@ class Configuration( object ): self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) ) self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) - self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' ) - self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) + self.support_url = kwargs.get( 'support_url', 'https://galaxyproject.org/support' ) + self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.biostar_url = kwargs.get( 'biostar_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) From 72cd0ba00ad05793751105dccf434c9868791b2a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 17 Mar 2017 20:24:09 +0100 Subject: [PATCH 06/14] Adjust link to the new Galaxy HUB site --- client/galaxy/scripts/mvc/workflow/workflow-forms.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js index 965f70db631..7ffe4611ec0 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js @@ -151,7 +151,7 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func type : 'text', value : '', ignore : '', - help : 'This action will rename the output dataset. Click here for more information. Valid inputs are: ' + input_terminal_names.join(', ') + '.' + help : 'This action will rename the output dataset. Click here for more information. Valid inputs are: ' + input_terminal_names.join(', ') + '.' },{ action : 'ChangeDatatypeAction', pja_arg : 'newtype', From ea3796152a01aad87f0585bf83ceb661392ba4d4 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 26 Apr 2017 16:55:00 -0400 Subject: [PATCH 07/14] Replace wiki.galaxyproject.org links in /lib --- lib/galaxy/web/base/controllers/admin.py | 2 +- lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py | 2 +- lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/web/base/controllers/admin.py b/lib/galaxy/web/base/controllers/admin.py index 115689af894..c1cfed50c13 100644 --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1044,7 +1044,7 @@ class Admin( object ): stop_msg += '.' for job_id in job_ids: error_msg = "This job was stopped by an administrator: %s Contact support for additional help." \ - % ( stop_msg, self.app.config.get("support_url", "https://wiki.galaxyproject.org/Support" ) ) + % ( stop_msg, self.app.config.get("support_url", "https://galaxyproject.org/support/" ) ) if trans.app.config.track_jobs_in_database: job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) job.stderr = error_msg diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py index 00f9d6025bb..d6c8ff31c8f 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -33,7 +33,7 @@ def get_message_for_no_shed_tool_config(): message += 'tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to ' message += 'automatically install tools from a tool shed into Galaxy (e.g., the file name shed_tool_conf.xml whose tag is ' message += '). For details, see the "Installation of Galaxy tool shed repository tools into a local ' - message += 'Galaxy instance" section of the Galaxy tool shed wiki at http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#' + message += 'Galaxy instance" section of the Galaxy tool shed wiki at https://galaxyproject.org/installing-repositories-to-galaxy/' message += 'Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance.' return message diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index e0742004dab..e607b83342c 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -961,7 +961,7 @@ class AdminToolshed( AdminGalaxy ): message += 'attribute value which is a directory relative to the Galaxy installation directory in order ' message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name shed_tool_conf.xml ' message += 'whose <toolbox> tag is <toolbox tool_path="../shed_tools">).

See the ' - message += 'Installation ' + message += 'Installation ' message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance section of the Galaxy Tool ' message += 'Shed wiki for all of the details.' return trans.show_error_message( message ) From 04a32064f1d553c01828092b445175a9c7d8a53d Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 26 Apr 2017 17:02:46 -0400 Subject: [PATCH 08/14] Update wiki.galaxyproject.org links in client --- .../scripts/mvc/library/library-foldertoolbar-view.js | 2 +- .../galaxy/scripts/mvc/library/library-librarylist-view.js | 2 +- .../scripts/mvc/library/library-librarytoolbar-view.js | 2 +- client/galaxy/scripts/mvc/tool/tool-form-base.js | 2 +- client/galaxy/scripts/mvc/user/user-preferences.js | 2 +- client/galaxy/scripts/viz/phyloviz.js | 2 +- static/maps/mvc/citation/citation-view.js.map | 2 +- static/maps/mvc/library/library-folderlist-view.js.map | 2 +- static/maps/mvc/library/library-foldertoolbar-view.js.map | 2 +- static/maps/mvc/library/library-librarylist-view.js.map | 2 +- static/maps/mvc/library/library-librarytoolbar-view.js.map | 2 +- static/maps/mvc/tool/tool-form-base.js.map | 2 +- static/maps/mvc/user/user-preferences.js.map | 2 +- static/maps/mvc/workflow/workflow-forms.js.map | 2 +- static/maps/viz/phyloviz.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 6 +++--- static/scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js | 2 +- static/scripts/bundled/libs.bundled.js.map | 2 +- static/scripts/bundled/login.bundled.js.map | 2 +- static/scripts/mvc/citation/citation-view.js | 2 +- static/scripts/mvc/library/library-folderlist-view.js | 2 +- static/scripts/mvc/library/library-foldertoolbar-view.js | 2 +- static/scripts/mvc/library/library-librarylist-view.js | 2 +- static/scripts/mvc/library/library-librarytoolbar-view.js | 2 +- static/scripts/mvc/tool/tool-form-base.js | 2 +- static/scripts/mvc/user/user-preferences.js | 2 +- static/scripts/mvc/workflow/workflow-forms.js | 2 +- static/scripts/viz/phyloviz.js | 2 +- 29 files changed, 31 insertions(+), 31 deletions(-) diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js index 411bad9fcf5..cf93c78e341 100644 --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -1144,7 +1144,7 @@ var FolderToolbarView = Backbone.View.extend({ ' Details', '', '', - '', + '', '', '', '', diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js index fb1c7d9af2d..6e5fa18b3a9 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-base.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js @@ -279,7 +279,7 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view _.each( options.requirements, function( req, i ) { requirements_message += req.name + ( req.version ? ' (Version ' + req.version + ')' : '' ) + ( i < nreq - 2 ? ', ' : ( i == nreq - 2 ? ' and ' : '' ) ); }); - var requirements_link = $( '' ).attr( 'target', '_blank' ).attr( 'href', 'https://wiki.galaxyproject.org/Tools/Requirements' ).text( 'here' ); + var requirements_link = $( '' ).attr( 'target', '_blank' ).attr( 'href', 'https://galaxyproject.org/tools/requirements/' ).text( 'here' ); return $( '' ).append( requirements_message + '. Click ' ).append( requirements_link ).append( ' for more information.' ); } return 'No requirements found.'; diff --git a/client/galaxy/scripts/mvc/user/user-preferences.js b/client/galaxy/scripts/mvc/user/user-preferences.js index 5d3e3438aec..d7bb7e19ded 100644 --- a/client/galaxy/scripts/mvc/user/user-preferences.js +++ b/client/galaxy/scripts/mvc/user/user-preferences.js @@ -187,7 +187,7 @@ define( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) { return '

' + 'You are using ' + options.nice_total_disk_usage + ' of disk space in this Galaxy instance. ' + ( Galaxy.config.enable_quotas ? 'Your disk quota is: ' + options.quota + '. ' : '' ) + - 'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.' + + 'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.' + '

'; } }); diff --git a/client/galaxy/scripts/viz/phyloviz.js b/client/galaxy/scripts/viz/phyloviz.js index 15a17a0909e..4fbc8d3f1e4 100644 --- a/client/galaxy/scripts/viz/phyloviz.js +++ b/client/galaxy/scripts/viz/phyloviz.js @@ -741,7 +741,7 @@ var HeaderButtons = Backbone.View.extend({ $("#nodeSelectionView").show(); } }, { icon_class: 'information', title: 'Phyloviz Help', on_click: function() { - window.open('https://wiki.galaxyproject.org/Learn/Visualization/PhylogeneticTree'); + window.open('https://galaxyproject.org/learn/visualization/phylogenetic-tree/'); // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs3EyMe1B1X_KFPouzIgrCz3zk/edit } } ], diff --git a/static/maps/mvc/citation/citation-view.js.map b/static/maps/mvc/citation/citation-view.js.map index 8454efa7beb..b67e2708532 100644 --- a/static/maps/mvc/citation/citation-view.js.map +++ b/static/maps/mvc/citation/citation-view.js.map @@ -1 +1 @@ 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").addClass("portlet-buttons"))).append(r("
").addClass("portlet-backdrop"))}});return{View:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},,function(e,t,i){var n,s;(function(o,a,r){n=[i(8),i(24),i(14)],s=function(e,t,i){var n=o.Model.extend({}),s=o.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.get("metadata")||this._set_metadata(),this.on("change",this._set_metadata,this)},_set_metadata:function(){var e=new n;a.each(a.keys(this.attributes),function(t){if(0===t.indexOf("metadata_")){var i=t.split("metadata_")[1];e.set(i,this.attributes[t]),delete this.attributes[t]}},this),this.set("metadata",e,{silent:!0})},get_metadata:function(e){return this.attributes.metadata.get(e)},urlRoot:Galaxy.root+"api/datasets"}),l=s.extend({defaults:a.extend({},s.prototype.defaults,{chunk_url:null,first_data_chunk:null,offset:0,at_eof:!1}),initialize:function(e){s.prototype.initialize.call(this),this.attributes.first_data_chunk&&(this.attributes.offset=this.attributes.first_data_chunk.offset),this.attributes.chunk_url=Galaxy.root+"dataset/display?dataset_id="+this.id,this.attributes.url_viz=Galaxy.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof)return null;var e=this,t=r.Deferred();return r.getJSON(this.attributes.chunk_url,{offset:e.attributes.offset}).success(function(i){var n;""!==i.ck_data?(n=i,e.attributes.offset=i.offset):(e.attributes.at_eof=!0,n=null),t.resolve(n)}),t}}),c=o.Collection.extend({model:s}),d=o.View.extend({initialize:function(e){this.row_count=0,this.loading_chunk=!1,new p({model:e.model,$el:this.$el})},expand_to_container:function(){this.$el.height()").attr("id","loading_indicator"),this.$el.append(this.loading_indicator);var e=r("").attr({id:"content_table",cellpadding:0});this.$el.append(e);var t=this.model.get_metadata("column_names"),i=r("").appendTo(e),n=r("").appendTo(i);if(t)n.append("");else for(var s=1;s<=this.model.get_metadata("columns");s++)n.append("");var o=this,a=this.model.get("first_data_chunk");a?this._renderChunk(a):r.when(o.model.get_next_chunk()).then(function(e){o._renderChunk(e)}),this.scroll_elt.scroll(function(){o.attempt_to_fetch()})},scrolled_to_bottom:function(){return!1},_renderCell:function(e,t,i){var n=r("");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=a("")},add:function(e,t,i){var n=a("");t&&n.css("width",t),i&&n.css("text-align",i),n.append(e),this.row.append(n)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$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.$tbody.find(".current").attr("id"),void 0!==e&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return void 0===t?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,i){this.del(e),this.row.attr("id",e),i?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return a('')},_onclick:function(e){var t=this.value(),i=a(e.target).closest("tr").attr("id");""!=i&&i&&t!=i&&(this.options.onconfirm?this.options.onconfirm(i):this.value(i))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){0==this.row_count?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'
"+t.join("")+""+s+"").text(e),s=this.model.get_metadata("column_types");return void 0!==i?n.attr("colspan",i).addClass("stringalign"):s&&t"),n=this.model.get_metadata("columns");return this.row_count%2!==0&&i.addClass("dark_row"),t.length===n?a.each(t,function(e,t){i.append(this._renderCell(e,t))},this):t.length>n?(a.each(t.slice(0,n-1),function(e,t){i.append(this._renderCell(e,t))},this),i.append(this._renderCell(t.slice(n-1).join("\t"),n-1))):1===t.length?i.append(this._renderCell(e,0,n)):(a.each(t,function(e,t){i.append(this._renderCell(e,t))},this),a.each(a.range(n-t.length),function(){i.append(r(""))})),this.row_count++,i},_renderChunk:function(e){var t=this.$el.find("table");a.each(e.ck_data.split("\n"),function(e,i){""!==e&&t.append(this._renderRow(e))},this)}}),h=d.extend({initialize:function(e){d.prototype.initialize.call(this,e),scroll_elt=a.find(this.$el.parents(),function(e){return"auto"===r(e).css("overflow")}),scroll_elt||(scroll_elt=window),this.scroll_elt=r(scroll_elt)},scrolled_to_bottom:function(){return this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),u=d.extend({initialize:function(e){d.prototype.initialize.call(this,e),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:e.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),p=o.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(e){function t(e,t){for(var i=0;i").attr("type","button").append(this.$icon=a("")).append(this.$title=a("")).append(this.$progress=a("
").append(this.$progress_bar=a("
")))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var e=this,t=this.model.attributes;this.$el.removeClass().addClass("ui-button-default").addClass(t.disabled&&"disabled").attr("id",t.id).attr("disabled",t.disabled).css("float",t.floating).off("click").on("click",function(){a(".tooltip").hide(),t.onclick&&!e.disabled&&t.onclick()}).tooltip({title:t.tooltip,placement:"bottom"}),this.$progress.addClass("progress").css("display",t.percentage!==-1?"block":"none"),this.$progress_bar.addClass("progress-bar").css({width:t.percentage+"%"}),this.$icon.removeClass().addClass("icon fa"),this.$title.removeClass().addClass("title"),t.wait?(this.$el.addClass(t.wait_cls).prop("disabled",!0),this.$icon.addClass("fa-spinner fa-spin ui-margin-right"),this.$title.html(t.wait_text)):(this.$el.addClass(t.cls),this.$icon.addClass(t.icon),this.$title.html(t.title),t.icon&&t.title&&this.$icon.addClass("ui-margin-right"))},show:function(){this.$el.show()},hide:function(){this.$el.hide()},disable:function(){this.model.set("disabled",!0)},enable:function(){this.model.set("disabled",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},setIcon:function(e){this.model.set("icon",e)}}),i=t.extend({initialize:function(t){this.model=t&&t.model||new o.Model({id:e.uid(),title:"",icon:"",cls:""}).set(t),this.setElement(a("").append(this.$icon=a(""))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var e=this.model.attributes;this.$el.removeClass().addClass(e.cls).attr({id:e.id,href:e.href||"javascript:void(0)",title:e.title,target:e.target||"_top",disabled:e.disabled}).off("click").on("click",function(){e.onclick&&!e.disabled&&e.onclick()}),this.$icon.removeClass().addClass(e.icon)}}),n=o.View.extend({initialize:function(t){this.model=t&&t.model||new o.Model({id:e.uid(),title:"Select/Unselect all",icons:["fa-square-o","fa-minus-square-o","fa-check-square-o"],value:0,onchange:function(){}}).set(t),this.setElement(a("
").append(this.$icon=a("")).append(this.$title=a(""))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(e){var t=this,e=this.model.attributes;this.$el.addClass("ui-button-check").off("click").on("click",function(){t.model.set("value",0===t.model.get("value")&&2||0),e.onclick&&e.onclick()}),this.$title.html(e.title),this.$icon.removeClass().addClass("icon fa ui-margin-right").addClass(e.icons[e.value])},value:function(e,t){return void 0!==e&&(t&&0!==e&&(e=e!==t&&1||2),this.model.set("value",e),this.model.get("onchange")(this.model.get("value"))),this.model.get("value")}}),s=t.extend({initialize:function(t){this.model=t&&t.model||new o.Model({id:e.uid(),title:"",floating:"right",icon:"",cls:"ui-button-icon",disabled:!1}).set(t),this.setElement(a("
").append(this.$button=a("
").append(this.$icon=a("")).append(this.$title=a("")))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(e){var e=this.model.attributes;this.$el.removeClass().addClass(e.cls).addClass(e.disabled&&"disabled").attr("disabled",e.disabled).attr("id",e.id).css("float",e.floating).off("click").on("click",function(){a(".tooltip").hide(),!e.disabled&&e.onclick&&e.onclick()}),this.$button.addClass("button").tooltip({title:e.tooltip,placement:"bottom"}),this.$icon.removeClass().addClass("icon fa").addClass(e.icon),this.$title.addClass("title").html(e.title),e.icon&&e.title&&this.$icon.addClass("ui-margin-right")}}),r=t.extend({$menu:null,initialize:function(e){this.model=e&&e.model||new o.Model({id:"",title:"",floating:"right",pull:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""}).set(e),this.collection=new o.Collection,this.setElement(a("
").append(this.$root=a("
").append(this.$icon=a("")).append(this.$title=a("")))),this.listenTo(this.model,"change",this.render,this),this.listenTo(this.collection,"change add remove reset",this.render,this),this.render()},render:function(){var e=this,t=this.model.attributes;this.$el.removeClass().addClass("dropdown").addClass(t.cls).attr("id",t.id).css({float:t.floating,display:t.visible&&this.collection.where({visible:!0}).length>0?"block":"none"}),this.$root.addClass("root button dropdown-toggle").attr("data-toggle","dropdown").tooltip({title:t.tooltip,placement:"bottom"}).off("click").on("click",function(e){a(".tooltip").hide(),e.preventDefault(),t.onclick&&t.onclick()}),this.$icon.removeClass().addClass("icon fa").addClass(t.icon),this.$title.removeClass().addClass("title").html(t.title),t.icon&&t.title&&this.$icon.addClass("ui-margin-right"),this.$menu&&this.$menu.remove(),this.collection.length>0&&(this.$menu=a("
","
"].join("")}});return{CitationView:n,CitationListView:s}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3))},function(e,t,i){var n,s;(function(o,a,r){n=[i(43),i(34),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=e.FoldoutListItemView,l=e.ListItemView,c=s.extend({className:s.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(e){this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,s.prototype.initialize.call(this,e)},_setUpListeners:function(){s.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(e,t){o.has(e.changed,"deleted")?this.render():o.has(e.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var e=s.prototype._getFoldoutPanelOptions.call(this);return o.extend(e,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var e=this.model?this.model+"":"(no model)";return"DCListItemView("+e+")"}});c.prototype.templates=function(){var e=o.extend({},s.prototype.templates.warnings,{error:i.wrapTemplate(["<% if( model.error ){ %>",'
',n("There was an error getting the data for this collection"),": <%- model.error %>","
","<% } %>"]),purged:i.wrapTemplate(["<% if( model.purged ){ %>",'
',n("This collection has been deleted and removed from disk"),"
","<% } %>"]),deleted:i.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
',n("This collection has been deleted"),"
","<% } %>"])}),t=i.wrapTemplate(['
','
','<%- collection.element_identifier || collection.name %>',"
",'
',"
"],"collection"),a=i.wrapTemplate(['
','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<% if( collection.collection_type === "list" ){ %>',n("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',n("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',n("a list of <%- countText %>dataset pairs"),'<% } else if( collection.collection_type === "list:list" ){ %>',n("a list of <%- countText %>dataset lists"),"<% } %>","
"],"collection");return o.extend({},s.prototype.templates,{warnings:e,titleBar:t,subtitle:a})}();var d=l.extend({className:l.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DCEListItemView.initialize:",e),l.prototype.initialize.call(this,e)},toString:function(){var e=this.model?this.model+"":"(no model)";return"DCEListItemView("+e+")"}});d.prototype.templates=function(){var e=i.wrapTemplate(['
','
','<%- element.element_identifier %>',"
",'
',"
"],"element");return o.extend({},l.prototype.templates,{titleBar:e})}();var h=t.DatasetListItemView.extend({className:t.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DatasetDCEListItemView.initialize:",e),t.DatasetListItemView.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):r.when()},toString:function(){var e=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+e+")"}});h.prototype.templates=function(){var e=i.wrapTemplate(['
','','
','<%- element.element_identifier %>',"
","
"],"element");return o.extend({},t.DatasetListItemView.prototype.templates,{titleBar:e})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(e){c.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+e+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(70),i(6),i(5)],s=function(e,t,i){"use strict";var n={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(e){return o.extend(e,e.object,{element_id:e.id}),delete e.object,e},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",a.Model.apply(this,arguments)},parse:function(e,t){var i=e;return i=this._mergeObject(i)}},s=a.Model.extend(t.LoggableMixin).extend(n).extend({_logNamespace:"collections"}),l=a.Collection.extend(t.LoggableMixin).extend({_logNamespace:"collections",model:s,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),c=e.DatasetAssociation.extend(t.mixin(n,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:o.extend({},e.DatasetAssociation.prototype.defaults,n.defaults),constructor:function(e,t){this.debug("\t DatasetDCE.constructor:",e,t),n.constructor.call(this,e,t)},hasDetails:function(){return this.elements&&this.elements.length},toString:function(){var e=this.get("element_identifier");return["DatasetDCE(",e,")"].join("")}})),d=l.extend({model:c,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=a.Model.extend(t.LoggableMixin).extend(t.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:l,initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var e=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(e),this.elements},toJSON:function(){var e=a.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=a.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var e=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+e.join(",")+")"}}),u=h.extend({collectionClass:d,toString:function(){return"List"+h.prototype.toString.call(this)}}),p=u.extend({toString:function(){return"Pair"+h.prototype.toString.call(this)}}),g=h.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",e,")"].join("")}})),f=l.extend({model:g,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=p.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedPairDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",e,")"].join("")}})),v=f.extend({model:m,toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),_=h.extend({collectionClass:v,toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}}),y=u.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedListDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedListDCDCE(",e,")"].join("")}})),w=f.extend({model:y,toString:function(){return["NestedListDCDCECollection(",this.length,")"].join("")}}),b=h.extend({collectionClass:w,toString:function(){return["ListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:u,PairDatasetCollection:p,ListPairedDatasetCollection:_,ListOfListsDatasetCollection:b}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3),i(1))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(40),i(12),i(6),i(8),i(88),i(5),i(85)],s=function(e,t,i,n,s,c){"use strict";function d(e){var t=e.toJSON(),i=f(t,{creationFn:function(t,i){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i)}});return i}var h="collections",u=o.View.extend(i.LoggableMixin).extend({_logNamespace:h,tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:a.template(['',"<%- element.name %>","",'"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([c("Enter a new name for the element"),":\n(",c("Note that changing the name here will not rename the dataset"),")"].join(""),prompt(c("Enter a new name for the 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creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;a.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=a.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var 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    ','','',"
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    ","
      ","
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    ","

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    ","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
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    ","<% }); %>"],"apps");return l.extend({},d.prototype.templates,{warnings:e,details:i,noAccess:o,summaries:a,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4)],s=function(e){var t=o.Model.extend({initialize:function(e){this.app=e},checksum:function(){var e="",t=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=t.app.field_list[i];n&&(e+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),e},create:function(){function e(e,t,i){n.flat_dict[e]=t,o[e]=i,n.app.element_list[t]&&n.app.element_list[t].$el.attr("tour_id",e)}function t(s,o){for(var a in o){var r=o[a];if(r.input){var l=r.input,c=s;switch(""!=s&&(c+="|"),c+=l.name,l.type){case"repeat":var d="section-",h=[],u=null;for(var p in r){var g=p.indexOf(d);g!=-1&&(g+=d.length,h.push(parseInt(p.substr(g))),u||(u=p.substr(0,g)))}h.sort(function(e,t){return e-t});var a=0;for(var f in h)t(c+"_"+a++,r[u+h[f]]);break;case"conditional":var m=n.app.field_list[l.id].value();e(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);v!=-1&&t(c,o[l.id+"-section-"+v]);break;case"section":t(!l.flat&&c||"",r);break;default:var _=n.app.field_list[l.id];if(_&&_.value){var m=_.value();if((void 0===l.ignore||l.ignore!=m)&&(_.collapsed&&l.collapsible_value&&(m=l.collapsible_value),e(c,l.id,m),l.payload))for(var y in l.payload)e(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},t("",s),o},match:function(e){return this.flat_dict&&this.flat_dict[e]},matchCase:function(e,t){return i(e,t)},matchModel:function(e,t){var i=this;n(e.inputs,function(e,n){i.flat_dict[n]&&t(e,i.flat_dict[n])})},matchResponse:function(e){function t(e,s){if("string"==typeof s){var o=n.flat_dict[e];o&&(i[o]=s)}else for(var a in s){var r=a;if(""!==e){var l="|";s instanceof Array&&(l="_"),r=e+l+r}t(r,s[a])}}var i={},n=this;return t("",e),i},_iterate:function(e,t){var i=this,n=a(e).children();n.each(function(){var e=this,n=a(e).attr("id");if(a(e).hasClass("section-row")){var s=i.app.input_list[n];t[n]=s&&{input:s}||{},i._iterate(e,t[n])}else i._iterate(e,t)})}}),i=function(e,t){"boolean"==e.test_param.type&&(t="true"==t?e.test_param.truevalue||"true":e.test_param.falsevalue||"false");for(var i in e.cases)if(e.cases[i].value==t)return i;return-1},n=function(e,t,s,o){o=a.extend(!0,{},o),r.each(e,function(e){e&&e.type&&e.name&&(o[e.name]=e)});for(var l in e){var c=e[l];c.name=c.name||l;var d=s?s+"|"+c.name:c.name;switch(c.type){case"repeat":r.each(c.cache,function(e,i){n(e,t,d+"_"+i,o)});break;case"conditional":if(c.test_param){t(c.test_param,d+"|"+c.test_param.name,o);var h=i(c,c.test_param.value);h!=-1?n(c.cases[h].inputs,t,d,o):Galaxy.emit.debug("form-data::visitInputs() - Invalid case for "+d+".")}else Galaxy.emit.debug("form-data::visitInputs() - Conditional test parameter missing for "+d+".");break;case"section":n(c.inputs,t,d,o);break;default:t(c,d,o)}}};return{Manager:t,visitInputs:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(i,o,a){n=[],s=function(){return i.View.extend({initialize:function(e,t){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=t&&t.field||new i.View,this.model=t&&t.model||new i.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up"}).set(t),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var s=this;this.$collapsible.on("click",function(){s.field.collapsed=!s.field.collapsed,e.trigger&&e.trigger("change"),s.render()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){o(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&e.indexOf("("+t+")")==-1&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(a.escape(this.model.get("text_value")));var i=this.model.get("error_text");if(this.$error[i?"show":"hide"](),this.$el[i?"addClass":"removeClass"]("ui-error"),this.$error_text.html(i),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var n=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+n)).attr("data-original-title",this.model.get("text_"+n)).tooltip({placement:"bottom"})}},_template:function(){return o("
    ").addClass("ui-form-element").append(o("
    ").addClass("ui-form-error ui-error").append(o("").addClass("fa fa-arrow-down")).append(o("").addClass("ui-form-error-text"))).append(o("
    ").addClass("ui-form-title").append(o("
    ").addClass("ui-form-collapsible").append(o("").addClass("ui-form-collapsible-icon")).append(o("").addClass("ui-form-collapsible-text"))).append(o("").addClass("ui-form-title-text"))).append(o("
    ").addClass("ui-form-field").append(o("").addClass("ui-form-info")).append(o("
    ").addClass("ui-form-backdrop"))).append(o("
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    ").append(this.$list=a("
    ")).append(a("
    ").append(this.button_new.$el)))},size:function(){return r.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var n=new i.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),s=new t.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:n}});s.append(e.$el),s.$el.addClass("section-row").hide(),this.list[e.id]=s,this.$list.append(s.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(e){return this.list[e]?(this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),void this._refresh()):void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.")},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(e){e.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("
    ").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});return{View:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(4),i(7),i(9),i(38),i(36),i(37)],s=function(e,t,i,n,s,c){var d=o.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new c,this.setElement(a("
    ")),this.render()},render:function(){var e=this;this.$el.empty(),r.each(this.inputs,function(t){e.add(t)})},add:function(t){var i=l.extend(!0,{},t);switch(i.id=t.id=e.uid(),this.app.input_list[i.id]=i,i.type){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.model.get("sustain_conditionals")&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var n=t.app.data.matchCase(e,i);for(var s in e.cases){var o=e.cases[s],a=t.$("#"+e.id+"-section-"+s),r=!1;for(var l in o.inputs)if(!o.inputs[l].hidden){r=!0;break}s==n&&r?a.fadeIn("fast"):a.hide()}t.app.trigger("change")});for(var n in e.cases){var s=new d(this.app,{inputs:e.cases[n].inputs});this._append(s.$el.addClass("ui-form-section"),e.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(e){function t(t){var n=e.id+"-section-"+o++,s=new d(i.app,{inputs:t});a.add({id:n,$el:s.$el,ondel:function(){a.del(n),i.app.trigger("change")}})}for(var i=this,o=0,a=new n.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),l=r.size(e.cache),c=0;c").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=e.onchange||function(){t.app.trigger("change",i)};var n=this.parameters.create(e);this.app.field_list[i]=n;var o=new s(this.app,{name:e.name,label:e.hide_label?"":e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,fixed:e.fixed,field:n});return this.app.element_list[i]=o,this._append(o.$el,e.id),n},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});return{View:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o){n=[i(32),i(74),i(5)],s=function(e,t,i){"use strict";function n(e){return function(t,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",t=t||{},t.type="dataset_collection"),e.call(this,t,i)}}var s=t.HistoryContentMixin,a=e.ListDatasetCollection,r=e.PairDatasetCollection,l=e.ListPairedDatasetCollection,c=e.ListOfListsDatasetCollection,d=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(a.prototype.save),toString:function(){return"History"+a.prototype.toString.call(this)}}),h=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(r.prototype.save),toString:function(){return"History"+r.prototype.toString.call(this)}}),u=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(l.prototype.save),toString:function(){return"History"+l.prototype.toString.call(this)}}),p=c.extend(s).extend({defaults:o.extend(o.clone(c.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(c.prototype.save),toString:function(){return["HistoryListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:d,HistoryPairDatasetCollection:h,HistoryListPairedDatasetCollection:u,HistoryListOfListsDatasetCollection:p}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(67),i(72),i(40),i(42),i(6),i(131)],s=function(e,t,i,n,s,l){"use strict";var c=e.PaginatedCollection,d=c.extend(s.LoggableMixin).extend({_logNamespace:"history",model:function(e,n){if("dataset"===e.history_content_type)return new t.HistoryDatasetAssociation(e,n);if("dataset_collection"===e.history_content_type){switch(e.collection_type){case"list":return new i.HistoryListDatasetCollection(e,n);case"paired":return new i.HistoryPairDatasetCollection(e,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(e,n);case"list:list":return new i.HistoryListOfListsDatasetCollection(e,n)}var s="Unknown collection_type: "+e.collection_type;return console.warn(s,e),{validationError:s}}return{validationError:"Unknown history_content_type: "+e.history_content_type}},limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){t=t||{},c.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},setHistoryId:function(e){this.historyId=e,this._setUpWebStorage()},_setUpWebStorage:function(e){if(this.historyId)return this.storage=new n.HistoryPrefs({id:n.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:o.extend(o.clone(c.prototype.comparators),{name:s.buildComparator("name",{ascending:!0}),"name-dsc":s.buildComparator("name",{ascending:!1}),hid:s.buildComparator("hid",{ascending:!1}),"hid-asc":s.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(e,t){if(o.isBoolean(e)&&e!==this.includeDeleted){if(this.includeDeleted=e,o.result(t,"silent"))return;this.trigger("include-deleted",e,this)}},setIncludeHidden:function(e,t){if(o.isBoolean(e)&&e!==this.includeHidden){if(this.includeHidden=e,t=t||{},o.result(t,"silent"))return;this.trigger("include-hidden",e,this)}},fetch:function(e){if(e=e||{},this.historyId&&!e.details){var t=n.HistoryPrefs.get(this.historyId).toJSON();o.isEmpty(t.expandedIds)||(e.details=o.values(t.expandedIds).join(","))}return c.prototype.fetch.call(this,e)},_buildFetchData:function(e){return o.extend(c.prototype._buildFetchData.call(this,e),{v:"dev"})},_fetchParams:c.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(e){var t=c.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted||(i.deleted=!1,i.purged=!1),this.includeHidden||(i.visible=!0),o.defaults(t,i)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(e){e=e||{};var t=this;return e.filters=o.extend(e.filters,{deleted:!0,purged:void 0}),e.remove=!1,t.trigger("fetching-deleted",t),t.fetch(e).always(function(){t.trigger("fetching-deleted-done",t)})},fetchHidden:function(e){e=e||{};var t=this;return e.filters=o.extend(e.filters,{visible:!1}),e.remove=!1,t.trigger("fetching-hidden",t),t.fetch(e).always(function(){t.trigger("fetching-hidden-done",t)})},fetchAllDetails:function(e){e=e||{};var t={details:"all"};return e.data=o.extend(e.data||{},t),this.fetch(e)},fetchCollectionCounts:function(e){return e=e||{},e.keys=["type_id","element_count"].join(","),e.filters=o.extend(e.filters||{},{history_content_type:"dataset_collection"}),e.remove=!1,this.fetch(e)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,s=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,s){var o=i.get(t[n]);return o?e.concat(o):e},[]),i.ajaxQueue("save",s,e)})},ajaxQueue:function(e,t,i){return i=i||this.models,new l.AjaxQueue(i.slice().reverse().map(function(i,n){var s=o.isString(e)?i[e]:e;return function(){return s.apply(i,t)}})).deferred},progressivelyFetchDetails:function(e){function i(t){t=t||0;var a=o.extend(o.clone(e),{view:"summary",keys:c,limit:r,offset:t,reset:0===t,remove:!1});o.defer(function(){s.fetch.call(s,a).fail(n.reject).done(function(e){n.notify(e,r,t),e.length!==r?(s.allFetched=!0,n.resolve(e,r,t)):i(t+r)})})}e=e||{};var n=a.Deferred(),s=this,r=e.limitPerCall||s.limitPerProgressiveFetch,l=t.HistoryDatasetAssociation.prototype.searchAttributes,c=l.join(",");return i(),n},isCopyable:function(e){var t=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return o.isObject(e)&&e.id&&o.contains(t,e.model_class)},copy:function(e){var t,i,n;o.isString(e)?(t=e,n="hda",i="dataset"):(t=e.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[e.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,r=a.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:t,source:n,type:i})}).done(function(e){s.add([e],{parse:!0})}).fail(function(e,o,a){s.trigger("error",s,r,{},"Error copying contents",{type:i,id:t,source:n})});return r},createHDCA:function(e,t,i,n){var s=this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,element_identifiers:e});return s.save(n)},haveSearchDetails:function(){return this.allFetched&&this.all(function(e){return o.has(e.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=r.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3))},function(e,t,i){var n,s;(function(o){n=[i(6)],s=function(e){"use strict";var t=e.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(e){return o.result(this.get("expandedIds"),e,!1)},allExpanded:function(){return o.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(e){ -return o.isUndefined(e)||this.set("show_deleted",e),this.get("show_deleted")},includeHidden:function(e){return o.isUndefined(e)||this.set("show_hidden",e),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return t.storageKeyPrefix+e},get:function(e){return new t({id:t.historyStorageKey(e)})},clearAll:function(e){for(var i in sessionStorage)0===i.indexOf(t.storageKeyPrefix)&&sessionStorage.removeItem(i)}});return{HistoryPrefs:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(e,t){"use strict";var i="list",n=o.View.extend(e.LoggableMixin).extend({_logNamespace:i,initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):a(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}}),s=n.extend(e.mixin(e.SelectableViewMixin,e.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(t){n.prototype.initialize.call(this,t),e.SelectableViewMixin.initialize.call(this,t),e.DraggableViewMixin.initialize.call(this,t),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=n.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return n.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=a('
    '),i=e.model.toJSON();return r.each(e.templates.warnings,function(n){t.append(a(n(i,e)))}),t},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){var t=32,i=13;return!e||"keydown"!==e.type||e.keyCode!==t&&e.keyCode!==i||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){var e=this.model?this.model+"":"(no model)";return"ListItemView("+e+")"}}));s.prototype.templates=function(){var t=e.wrapTemplate(['
    ','
    ','
    ','',"
    ",'
    ','
    ','
    ',"
    "]),i={},n=e.wrapTemplate(['
    ','','
    ','<%- element.name %>',"
    ",'
    ',"
    "],"element"),s=e.wrapTemplate(['
    ']),o=e.wrapTemplate(['
    ']);return{el:t,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var e=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e),n=new t(r.extend(i,{model:e}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});return c.prototype.templates=function(){var t=e.wrapTemplate(['
    ',"
    "],"collection");return r.extend({},s.prototype.templates,{details:t})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(4),i(55),i(7),i(23),i(17),i(30)],s=function(e,t,i,n,s,r){return n.extend({initialize:function(e){var i=this;this.deferred=new t,n.prototype.initialize.call(this,e),this.model.get("inputs")?this._buildForm(this.model.attributes):this.deferred.execute(function(e){i._buildModel(e,i.model.attributes,!0)}),this.model.get("listen_to_history")&&parent.Galaxy&&parent.Galaxy.currHistoryPanel&&this.listenTo(parent.Galaxy.currHistoryPanel.collection,"change",function(){i.model.get("onchange")()}),this.$el.on("remove",function(){i.remove()})},remove:function(){var e=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(e),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var t=this;this.model.set(e),this.model.set({title:e.title||""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:!this.model.get("hide_operations")&&this._operations(),onchange:function(){t.deferred.reset(),t.deferred.execute(function(e){t.model.get("postchange")(e,t)})}}),this.model.get("customize")&&this.model.get("customize")(this),this.render(),this.model.get("collapsible")||this.$el.append(o("
    ").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(t,n,s){var a=this,r=this.model.attributes;r.version=n.version,r.id=n.id;var l="",c={};r.job_id?l=Galaxy.root+"api/jobs/"+r.job_id+"/build_for_rerun":(l=Galaxy.root+"api/tools/"+r.id+"/build",Galaxy.params&&Galaxy.params.tool_id==r.id&&(c=o.extend({},Galaxy.params),r.version&&(c.tool_version=r.version))),e.get({url:l,data:c,success:function(e){return e.display?(a._buildForm(e),!s&&a.message.update({status:"success",message:"Now you are using '"+r.name+"' version "+r.version+", id '"+r.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",e),void t.resolve()):void(window.location=Galaxy.root)},error:function(e,n){var s=e&&e.err_msg||"Uncaught error.";401==n?window.location=Galaxy.root+"user/login?"+o.param({redirect:Galaxy.root+"?tool_id="+r.id}):a.$el.is(":empty")?a.$el.prepend(new i.Message({message:s,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:s,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",e),t.reject()}})},_operations:function(){var t=this,n=this.model.attributes,s=new i.ButtonMenu({icon:"fa-cubes",title:!n.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!n.sustain_version&&n.versions&&n.versions.length>1)for(var o in n.versions){var a=n.versions[o];a!=n.version&&s.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var e=n.id.replace(n.version,this.version),i=this.version;t.deferred.reset(),t.deferred.execute(function(n){t._buildModel(n,{id:e,version:i})})}})}else s.$el.hide();var r=new i.ButtonMenu({icon:"fa-caret-down",title:!n.narrow&&"Options"||null,tooltip:"View available options"});return n.biostar_url&&(r.addMenu({icon:"fa-question-circle",title:"Question?",onclick:function(){window.open(n.biostar_url+"/p/new/post/")}}),r.addMenu({icon:"fa-search",title:"Search",onclick:function(){window.open(n.biostar_url+"/local/search/page/?q="+n.name)}})),r.addMenu({icon:"fa-share",title:"Share",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+n.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&(r.addMenu({icon:"fa-download",title:"Download",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+n.id+"/download"}}),r.addMenu({icon:"fa-refresh",title:"Reload XML",onclick:function(){e.get({url:Galaxy.root+"api/tools/"+n.id+"/reload",success:function(e){t.message.update({persistent:!1,message:"Tool XML has been reloaded.",status:"success"})},error:function(e){t.message.update({persistent:!1,message:e.err_msg,status:"danger"})}})}})),n.requirements&&n.requirements.length>0&&r.addMenu({icon:"fa-info-circle",title:"Requirements",onclick:function(){!this.requirements_visible||t.portlet.collapsed?(this.requirements_visible=!0,t.portlet.expand(),t.message.update({persistent:!0,message:t._templateRequirements(n),status:"info"})):(this.requirements_visible=!1,t.message.update({message:""}))}}),n.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",onclick:function(){window.open(n.sharable_url)}}),{menu:r,versions:s}},_footer:function(){var e=this.model.attributes,t=o("
    ").append(this._templateHelp(e));if(e.citations){var i=o("
    "),n=new s.ToolCitationCollection;n.tool_id=e.id;var a=new r.CitationListView({el:i,collection:n});a.render(),n.fetch(),t.append(i)}return t},_templateHelp:function(e){var t=o("
    ").addClass("ui-form-help").append(e.help);return t.find("a").attr("target","_blank"),t},_templateRequirements:function(e){var t=e.requirements.length;if(t>0){var i="This tool requires ";a.each(e.requirements,function(e,n){i+=e.name+(e.version?" (Version "+e.version+")":"")+(n").attr("target","_blank").attr("href","https://wiki.galaxyproject.org/Tools/Requirements").text("here");return o("").append(i+". Click ").append(n).append(" for more information.")}return"No requirements found."}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(2),i(16),i(11),i(18)],s=function(e,t,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},r=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(e){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new r(this.toJSON())},set_value:function(e){this.set("value",e||"")}}),l=o.Collection.extend({model:r}),c=r.extend({}),d=r.extend({set_value:function(e){this.set("value",parseInt(e,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=d.extend({set_value:function(e){this.set("value",parseFloat(e))}}),u=r.extend({get_samples:function(){return e.map(this.get("options"),function(e){return e[0]})}});r.subModelTypes={integer:d,float:h,data:c,select:u};var p=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(t){this.set("inputs",new l(e.map(t.inputs,function(e){var t=r.subModelTypes[e.type]||r;return new t(e)})))},toJSON:function(){var e=o.Model.prototype.toJSON.call(this);return e.inputs=this.get("inputs").map(function(e){return e.toJSON()}),e},remove_inputs:function(e){var t=this,i=t.get("inputs").filter(function(t){return e.indexOf(t.get("type"))!==-1});t.get("inputs").remove(i)},copy:function(e){var t=new p(this.toJSON());if(e){var i=new o.Collection;t.get("inputs").each(function(e){e.get_samples()&&i.push(e)}),t.set("inputs",i)}return t},apply_search_results:function(t){return e.indexOf(t,this.attributes.id)!==-1?this.show():this.hide(),this.is_visible()},set_input_value:function(e,t){this.get("inputs").find(function(t){return t.get("name")===e}).set("value",t)},set_input_values:function(t){var i=this;e.each(e.keys(t),function(e){i.set_input_value(e,t[e])})},run:function(){return this._run()},rerun:function(e,t){return this._run({action:"rerun",target_dataset_id:e.id,regions:t})},get_inputs_dict:function(){var e={};return this.get("inputs").each(function(t){e[t.get("name")]=t.get("value")}),e},_run:function(n){var s=e.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new t.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});return a.when(r.go()).then(function(e){o.resolve(new i.DatasetCollection(e))}),o}});e.extend(p.prototype,s);var g=(o.View.extend({}),o.Collection.extend({model:p})),f=o.Model.extend(s),m=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){e.each(this.attributes.elems,function(e){e.show()}),this.show(),this.set("open",!1)},apply_search_results:function(t){var i,n=!0;e.each(this.attributes.elems,function(e){e instanceof f?(i=e,i.hide()):e instanceof p&&e.apply_search_results(t)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});e.extend(m.prototype,s);var v=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var e=this.attributes.query;if(e.length");e.append(k.tool_link(this.model.toJSON()));var t=this.model.get("form_style",null);if("upload1"===this.model.id)e.find("a").on("click",function(e){e.preventDefault(),Galaxy.upload.show()});else if("regular"===t){var i=this;e.find("a").on("click",function(e){e.preventDefault();var t=new n.View({id:i.model.id,version:i.model.get("version")});t.deferred.execute(function(){Galaxy.app.display(t)})})}return this.$el.append(e),this}}),b=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a("").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(k.panel_section(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");return e.each(this.model.attributes.elems,function(e){if(e instanceof p){var i=new w({model:e,className:"toolTitle"});i.render(),t.append(i.$el)}else if(e instanceof f){var n=new b({model:e});n.render(),t.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),C=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(k.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),a("#messagebox").is(":visible")&&this.$el.css("top","95px"),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(e){return this.model.attributes.clear_key&&this.model.attributes.clear_key===e.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),$=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var e=this,t=new C({model:this.model.get("tool_search")});return t.render(),e.$el.append(t.$el),this.model.get("layout").each(function(t){if(t instanceof m){var i=new x({model:t});i.render(),e.$el.append(i.$el)}else if(t instanceof p){var n=new w({model:t,className:"toolTitleNoSection"});n.render(),e.$el.append(n.$el)}else if(t instanceof f){var s=new b({model:t});s.render(),e.$el.append(s.$el)}}),e.$el.find("a.tool-link").click(function(t){var i=a(this).attr("class").split(/\s+/)[0],n=e.model.get("tools").get(i);e.trigger("tool_link_click",t,n)}),this},handle_search_results:function(){var e=this.model.get("tool_search").get("results");e&&0===e.length?a("#search-no-results").show():a("#search-no-results").hide()}}),E=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(k.tool_form(this.model.toJSON()))}}),k=(o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var e=this;this.tool_panel_view.on("tool_link_click",function(t,i){t.preventDefault(),e.show_tool(i)})},show_tool:function(e){var t=this;e.fetch().done(function(){t.tool_form_view.model=e,t.tool_form_view.render(),t.tool_form_view.$el.show(),a("#left").width("650px")})}}),{tool_search:e.template(['',' ',''].join("")),panel_section:e.template(['
    ','<%- name %>',"
    ",'
    '+e.content+"
    "}});return{View:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(i){n=[],s=function(){var e=i.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),t=i.Collection.extend({model:e});return{Model:e,Collection:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3))},,function(e,t,i){var n,s;(function(o,a){n=[i(4)],s=function(e){return o.Model.extend({initialize:function(){this.active={},this.last=null},execute:function(t){var i=this,n=e.uid(),s=t.length>0;this.active[n]=!0;var o=a.Deferred();o.promise().always(function(){delete i.active[n],s&&Galaxy.emit.debug("deferred::execute()",this.state().charAt(0).toUpperCase()+this.state().slice(1)+" "+n)}),a.when(this.last).always(function(){i.active[n]?(s&&Galaxy.emit.debug("deferred::execute()","Running "+n),t(o),!s&&o.resolve()):o.reject()}),this.last=o.promise()},reset:function(){Galaxy.emit.debug("deferred::execute()","Reset");for(var e in this.active)this.active[e]=!1},ready:function(){return a.isEmptyObject(this.active)}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},,,,,,,,,,,function(e,t,i){var n,s;(function(o,a){n=[i(6),i(5),i(15)],s=function(e,t){var i=o.View.extend(e.LoggableMixin).extend(e.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var e=this.model.get("annotation");return['",'
    ',a.escape(e),"
    "].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2))},function(e,t,i){var n,s;(function(o){n=[i(2),i(3),i(6)],s=function(e,t,i){"use strict";var n=t.Collection.extend({initialize:function(e,i){t.Collection.prototype.initialize.call(this,e,i),this.setOrder(i.order||this.order,{silent:!0})},_setUpListeners:function(){return this.on({"changed-order":this.sort})},fetch:function(e){return e=this._buildFetchOptions(e),t.Collection.prototype.fetch.call(this,e)},_buildFetchOptions:function(t){t=e.clone(t)||{};var i=this;t.traditional=!0,t.data=t.data||i._buildFetchData(t);var n=this._buildFetchFilters(t);return e.isEmpty(n)||e.extend(t.data,this._fetchFiltersToAjaxData(n)),t},_buildFetchData:function(t){var i={};return this.order&&(i.order=this.order),e.defaults(e.pick(t,this._fetchParams),i)},_fetchParams:["order","limit","offset","view","keys"],_buildFetchFilters:function(t){return e.clone(t.filters||{})},_fetchFiltersToAjaxData:function(t){var i={q:[],qv:[]};return e.each(t,function(e,t){void 0!==e&&""!==e&&(e===!0&&(e="True"),e===!1&&(e="False"),null===e&&(e="None"),i.q.push(t),i.qv.push(e))}),i},reset:function(e,i){return this.allFetched=!1,t.Collection.prototype.reset.call(this,e,i)},order:null,comparators:{update_time:i.buildComparator("update_time",{ascending:!1}),"update_time-asc":i.buildComparator("update_time",{ascending:!0}),create_time:i.buildComparator("create_time",{ascending:!1}),"create_time-asc":i.buildComparator("create_time",{ascending:!0})},setOrder:function(t,i){i=i||{};var n=this,s=n.comparators[t];if(e.isUndefined(s))throw new Error("unknown order: "+t);if(s!==n.comparator){n.order;return n.order=t,n.comparator=s,i.silent||n.trigger("changed-order",i),n}}}),s=n.extend({limitPerPage:500,initialize:function(e,t){n.prototype.initialize.call(this,e,t),this.currentPage=t.currentPage||0},getTotalItemCount:function(){return this.length},shouldPaginate:function(){return this.getTotalItemCount()>=this.limitPerPage},getLastPage:function(){return Math.floor(this.getTotalItemCount()/this.limitPerPage)},getPageCount:function(){return this.getLastPage()+1},getPageLimitOffset:function(e){return e=this.constrainPageNum(e),{limit:this.limitPerPage,offset:e*this.limitPerPage}},constrainPageNum:function(e){return Math.max(0,Math.min(e,this.getLastPage()))},fetchPage:function(t,i){var n=this;return t=n.constrainPageNum(t),n.currentPage=t,i=e.defaults(i||{},n.getPageLimitOffset(t)),n.trigger("fetching-more"),n.fetch(i).always(function(){n.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),a=n.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){n.prototype.initialize.call(this,e,t),this.limitOnFirstFetch=t.limitOnFirstFetch||this.limitOnFirstFetch,this.limitPerFetch=t.limitPerFetch||this.limitPerFetch,this.allFetched=!1,this.lastFetched=t.lastFetched||0},_buildFetchOptions:function(e){return e.remove=e.remove||!1,n.prototype._buildFetchOptions.call(this,e)},fetchFirst:function(t){return t=t?e.clone(t):{},this.allFetched=!1,this.lastFetched=0,this.fetchMore(e.defaults(t,{reset:!0,limit:this.limitOnFirstFetch}))},fetchMore:function(t){t=e.clone(t||{});var i=this;if(!t.reset&&i.allFetched)return o.when();t.offset=t.reset?0:t.offset||i.lastFetched;var n=t.limit=t.limit||i.limitPerFetch||null;return i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")}).done(function(t){var s=e.isArray(t)?t.length:0;i.lastFetched+=s,(!n||s .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});l.prototype.templates=function(){var e=n.wrapTemplate(['
    ','
    ','','',s("Back to "),"<%- view.parentName %>","","
    ",'
    ','
    <%- collection.name || collection.element_identifier %>
    ','
    ','<% if( collection.collection_type === "list" ){ %>',s("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',s("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',s("a list of paired datasets"),'<% } else if( collection.collection_type === "list:list" ){ %>',s("a list of dataset lists"),"<% } %>","
    ","
    ","
    "],"collection");return o.extend(o.clone(r.prototype.templates),{controls:e})}();var c=l.extend({DatasetDCEViewClass:i.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),d=c.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),h=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}}),u=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfListsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:l,ListCollectionView:c,PairCollectionView:d,ListOfPairsCollectionView:h,ListOfListsCollectionView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(12),i(34),i(77),i(66),i(22),i(6),i(5)],s=function(e,t,n,s,r,l,c){"use strict";var d=t.DatasetListItemView,h=d.extend({initialize:function(e){d.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var t=d.prototype._renderPrimaryActions.call(this);return this.model.get("state")===e.NOT_VIEWABLE?t:d.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===e.DISCARDED||!this.model.get("accessible"))return null;var t=this.model.get("purged"),i=this.model.get("deleted"),n={title:c("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return i||t?(n.disabled=!0,t?n.title=c("Cannot edit attributes of datasets removed from disk"):i&&(n.title=c("Undelete dataset to edit attributes"))):o.contains([e.UPLOAD,e.NEW],this.model.get("state"))&&(n.disabled=!0,n.title=c("This dataset is not yet editable")),r(n)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return r({title:c(t?"Dataset is already deleted":"Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=d.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&o.contains([e.OK,e.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,n=function(t){var n='
    ';t.name&&t.help?(n+="Tool help for "+t.name+"
    ",n+=t.help):n+="Tool help is unavailable for this dataset.
    ",n+="
    ",i.$el.find(".details").append(a.parseHTML(n))},s=function(e){a.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){n(e)}).fail(function(){n({})})};return null===Galaxy.user.id?null:r({title:"Tool Help",classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():a.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){s(e)}).fail(function(){console.log('Failed at recovering job information from the Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var t=d.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case e.UPLOAD:case e.NOT_VIEWABLE:return t;case e.ERROR:return t.unshift(this._renderErrButton()),t.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case e.OK:case e.FAILED_METADATA:return t.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return t.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){return r({title:c("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return r({title:c("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){t.preventDefault(),!function(){var t=[i(18)];(function(t){var i=new t.View({job_id:e});i.deferred.execute(function(){Galaxy.app.display(i)})}).apply(null,t)}()}})},_renderVisualizationsButton:function(){var e=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||o.isEmpty(e))return null;if(!o.isObject(e[0]))return this.warn("Visualizations have been switched off"),null;var t=a(this.templates.visualizations(e,this));return t.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(t.find(".visualization-link").addBack(".visualization-link")),t},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:a(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new n.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:r({title:c("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new s.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:r({title:c("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=a('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);e.find(".dbkey .value").replaceWith(t)}},events:o.extend(o.clone(d.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm(c("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAEditView("+e+")"}});return h.prototype.templates=function(){var e=o.extend({},d.prototype.templates.warnings,{failed_metadata:l.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
    ',c("An error occurred setting the metadata for this dataset"),'
    ',c("Set it manually or retry auto-detection"),"","
    ","<% } %>"],"dataset"),deleted:l.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
    ',c("This dataset has been deleted"),'
    ',c("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
    ',c("Permanently remove it from disk"),"","<% } %>","
    ","<% } %>"],"dataset")}),t=l.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
    ','','',"",'","
    ","<% } %>"],"visualizations");return o.extend({},d.prototype.templates,{warnings:e,visualizations:t})}(),{DatasetListItemEdit:h}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(12),i(6),i(5)],s=function(e,t,i){"use strict";var n="dataset",s=t.SearchableModelMixin,l=o.Model.extend(t.LoggableMixin).extend(t.mixin(s,{_logNamespace:n,defaults:{state:e.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(t,i){this.debug(this+"(Dataset).initialize",t,i), //!! this state is not in trans.app.model.Dataset.states - set it here - this.get("accessible")||this.set("state",e.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var e=this.get("id");if(!e)return{};var t={purge:"datasets/"+e+"/purge_async",display:"datasets/"+e+"/display/?preview=True",edit:"datasets/"+e+"/edit",download:"datasets/"+e+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+e,rerun:"tool_runner/rerun?id="+e,show_params:"datasets/"+e+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+e+"&metadata_name="};return a.each(t,function(e,i){t[i]=Galaxy.root+e}),this.urls=t,t},_setUpListeners:function(){this.on("change:state",function(e,t){this.log(this+" has changed state:",e,t),this.inReadyState()&&this.trigger("state:ready",e,t,this.previous("state"))}),this.on("change:id change:file_ext",function(e){this._generateUrls()})},toJSON:function(){var e=o.Model.prototype.toJSON.call(this);return a.extend(e,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var t=a.contains(e.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||t},hasDetails:function(){return!this.get("accessible")||this.has("annotation")},hasData:function(){return this.get("file_size")>0},fetch:function(e){var t=this;return o.Model.prototype.fetch.call(this,e).always(function(){t._generateUrls()})},parse:function(e,t){var i=o.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},save:function(e,t){return t=t||{},t.wait=!!a.isUndefined(t.wait)||t.wait,o.Model.prototype.save.call(this,e,t)},delete:function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},purge:function(e){if(this.get("purged"))return r.when();e=e||{},e.url=this.urls.purge;var t=this,n=r.ajax(e);return n.done(function(e,i,n){t.set({deleted:!0,purged:!0})}),n.fail(function(n,s,o){var a=i("Unable to purge dataset"),r="Removal of datasets by users is not allowed in this Galaxy instance";n.responseJSON&&n.responseJSON.error?a=n.responseJSON.error:n.responseText.indexOf(r)!==-1&&(a=r),n.responseText=a,t.trigger("error",t,n,e,i(a),{error:a})}),n},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 e=this.get("id")||"";return this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),c=o.Collection.extend(t.LoggableMixin).extend({_logNamespace:n,model:l,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=e.call(a,t);l.done(function(e){i.notify({curr:r,total:n,response:e,model:a})}),l.always(function(e){s.push(e),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},matches:function(e){return this.filter(function(t){return t.matches(e)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});return{DatasetAssociation:l,DatasetAssociationCollection:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(o){n=[i(34),i(6),i(5)],s=function(e,t,i){"use strict";var n=e.DatasetListItemView,s=n.extend({className:n.prototype.className+" history-content",initialize:function(e,t){n.prototype.initialize.call(this,e,t)},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAListItemView("+e+")"}});return s.prototype.templates=function(){var e=t.wrapTemplate(['
    ','','
    ','<%- dataset.hid %> ','<%- dataset.name %>',"
    ","
    ",'',"<% _.each(dataset.nametags, function(tag){ %>",'<%- tag %>',"<% }); %>","","
    "],"dataset"),s=o.extend({},n.prototype.templates.warnings,{hidden:t.wrapTemplate(["<% if( !dataset.visible ){ %>",'
    ',i("This dataset has been hidden"),"
    ","<% } %>"],"dataset")});return o.extend({},n.prototype.templates,{titleBar:e,warnings:s})}(),{HDAListItemView:s}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o){n=[i(70),i(74),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=e.DatasetAssociation,a=t.HistoryContentMixin,r=s.extend(i.mixin(a,{defaults:o.extend({},s.prototype.defaults,a.defaults,{history_content_type:"dataset",model_class:"HistoryDatasetAssociation"})}));return{HistoryDatasetAssociation:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o){n=[i(12),i(31),i(68),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var a=t.DCListItemView,r=a.extend({className:a.prototype.className+" history-content",_setUpListeners:function(){a.prototype._setUpListeners.call(this),this.listenTo(this.model,{"change:populated change:visible":function(e,t){this.render()}})},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return i.ListCollectionView;case"paired":return i.PairCollectionView;case"list:paired":return i.ListOfPairsCollectionView;case"list:list":return i.ListOfListsCollectionView}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(t){a.prototype._swapNewRender.call(this,t);var i=this.model.get("populated")?e.OK:e.RUNNING;return this.$el.addClass("state-"+i),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDCAListItemView("+e+")"}});return r.prototype.templates=function(){var e=o.extend({},a.prototype.templates.warnings,{hidden:n.wrapTemplate(["<% if( !collection.visible ){ %>",'
    ',s("This collection has been hidden"),"
    ","<% } %>"],"collection")}),t=n.wrapTemplate(['
    ','','
    ','<%- collection.hid %> ','<%- collection.name %>',"
    ",'
    ',"
    "],"collection");return o.extend({},a.prototype.templates,{warnings:e,titleBar:t})}(),{HDCAListItemView:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o){n=[i(12),i(6),i(5)],s=function(e,t,i){"use strict";var n={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",hidden:function(){return!this.get("visible")},isVisible:function(e,t){var i=!0;return e||!this.get("deleted")&&!this.get("purged")||(i=!1),t||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var e=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return e},hide:function(e){return this.get("visible")?this.save({visible:!1},e):o.when()},unhide:function(e){return this.get("visible")?o.when():this.save({visible:!0},e)},toString:function(){return[this.get("type_id"),this.get("hid"),this.get("name")].join(":")}};return{HistoryContentMixin:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(41),i(42),i(67),i(4),i(6),i(5)],s=function(e,t,i,n,s,c){"use strict";var d=o.Model.extend(s.LoggableMixin).extend(s.mixin(s.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:e.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(e,t){t=t||{},this.logger=t.logger||null,this.log(this+".initialize:",e,t),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:t.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(e,t,i,n,s){this.clearUpdateTimeout()},"change:id":function(e,t){this.contents&&(this.contents.historyId=t)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,a.makeArray(arguments))}}):this},contentsShown:function(){var e=this.get("contents_active"),t=e.active||0;return t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?n.bytesToString(e,!0,2):c("(empty)")},toJSON:function(){return r.extend(o.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(e){return"nice_size"===e?this.nice_size():o.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:l.param({keys:e.join(",")})})},refresh:function(e){e=e||{};var t=this,i=t.lastUpdateTime;this.contents.allFetched=!1;var n=0!==t.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)};return n().done(function(i,n,s){var o;try{o=new Date(s.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=o||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){function t(){n.clearUpdateTimeout(),n.updateTimeoutId=setTimeout(function(){n.refresh(e)},i)}e=e||{};var i=this.UPDATE_DELAY,n=this;if(n.id){var s=this.numOfUnfinishedShownContents();s>0?t():n._fetchContentRelatedAttributes().done(function(e){n.numOfUnfinishedJobs()>0?t():n.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},parse:function(e,t){var i=o.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?a.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?a.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):a.when()},copy:function(e,t,i){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var n={history_id:this.id};e&&(n.current=!0),t&&(n.name=t),i||(n.all_datasets=!1),n.view="dev-detailed";var s=this,o=a.post(this.urlRoot,n);return e?o.then(function(e){var t=new d(e);return t.setAsCurrent().done(function(){s.trigger("copied",s,e)})}):o.done(function(e){s.trigger("copied",s,e)})},setAsCurrent:function(){var e=this,t=a.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),h=i.InfinitelyScrollingCollection,u=h.extend(s.LoggableMixin).extend({_logNamespace:"history",model:d,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),h.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new d(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return r.extend(h.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=h.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),r.defaults(t,i)},fetchFirst:function(e){var t=this,i=l.when();return this.currentHistoryId&&(i=h.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:r.extend(r.clone(h.prototype.comparators),{name:s.buildComparator("name",{ascending:!0}),"name-dsc":s.buildComparator("name",{ascending:!1}),size:s.buildComparator("size",{ascending:!1}),"size-asc":s.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return h.prototype.sort.call(this,r.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,n){var s=this,o=a.getJSON(Galaxy.root+"history/create_new_current");return o.done(function(e){s.setCurrent(new d(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});return{History:d,HistoryCollection:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(43),i(129),i(6),i(5),i(86)],s=function(e,t,i,n){"use strict";var s="list",l=o.View.extend(i.LoggableMixin).extend({_logNamespace:s,viewClass:e.ListItemView,collectionClass:o.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:n("This list is empty"),noneFoundMsg:n("No matching items found"),searchPlaceholder:n("search"),initialize:function(e,t){e=e||{},e.logger&&(this.logger=e.logger),this.log(this+".initialize:",e),this.fxSpeed=a.has(e,"fxSpeed")?e.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=e.searchFor||"",this.selecting=void 0===e.selecting||e.selecting,this.selected=e.selected||[],this.lastSelected=null,this.dragItems=e.dragItems||!1,this.viewClass=e.viewClass||this.viewClass,this.views=[],this.collection=e.collection||this._createDefaultCollection(),this.filters=e.filters||[],this.$scrollContainer=e.$scrollContainer||this.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return this.off(),this.on({error:function(e,t,i,n,s){console.error(e,t,i,n,s)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_createDefaultCollection:function(){return new this.collectionClass([])},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.stopListening(this.collection),this.listenTo(this.collection,{error:function(e,t,i,n,s){this.trigger("error",e,t,i,n,s)},update:function(e,t){var i=t.changes;return t.renderAll||i.added.length+i.removed.length>1?this.renderItems():1===i.added.length?this.addItemView(a.first(i.added),e,t):1===i.removed.length?this.removeItemView(a.first(i.removed),e,t):void 0}}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(e,t){if(t&&t.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(e,i)}else t&&t.altKey&&!this.selecting&&this.showSelectors();this.selected.push(e.model.id),this.lastSelected=e.model.id},"view:de-selected":function(e,t){this.selected=a.without(this.selected,e.model.id)}})},render:function(e){this.log(this+".render",e);var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var e=r(this.templates.el({},this));return this._renderControls(e),this._renderTitle(e),this._renderSubtitle(e),this._renderSearch(e),this.renderItems(e),e},_renderControls:function(e){this.debug(this+"(ListPanel)._renderControls");var t=r(this.templates.controls({},this));return e.find(".controls").replaceWith(t),t},_renderTitle:function(e){},_renderSubtitle:function(e){},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),r(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",this.className).append(e.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(e){return e=e||this.$el,this.$controls(e).find("[title]").tooltip(),this._renderMultiselectActionMenu(e),this},_renderMultiselectActionMenu:function(e){e=e||this.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var s=r(['
    ','",'","
    "].join("")),o=i.map(function(e){var t=['
  • ',e.html,"
    • "].join("");return r(t).click(function(t){return t.preventDefault(),e.func(t)})});return s.find("ul").append(o),t.replaceWith(s),s},multiselectActions:function(){return[]},$scrollContainer:function(e){return(e||this.$el).parent().parent()},$controls:function(e){return(e||this.$el).find("> .controls")},$list:function(e){return(e||this.$el).find("> .list-items")},$messages:function(e){return(e||this.$el).find("> .controls .messages")},$emptyMessage:function(e){return(e||this.$el).find("> .empty-message")},renderItems:function(e){e=e||this.$el;var t=this;t.log(this+".renderItems",e);var i=t.$list(e);t.freeViews();var n=t._filterCollection();return t.views=n.map(function(e){var i=t._createItemView(e);return i}),i.empty(),t.views.length&&t._attachItems(e),t._renderEmptyMessage(e).toggle(!t.views.length),t.trigger("views:ready",t.views),t.views},_filterCollection:function(){var e=this;return e.collection.filter(a.bind(e._filterItem,e))},_filterItem:function(e){var t=this;return a.every(t.filters.map(function(t){return t.call(e)}))&&(!t.searchFor||e.matchesAll(t.searchFor))},_createItemView:function(e){var t=this._getItemViewClass(e),i=a.extend(this._getItemViewOptions(e),{model:e}),n=new t(i);return this._setUpItemViewListeners(n),n},_destroyItemView:function(e){this.stopListening(e),this.views=a.without(this.views,e)},_destroyItemViews:function(e){var t=this;return t.views.forEach(function(e){t.stopListening(e)}),t.views=[],t},freeViews:function(){return this._destroyItemViews()},_getItemViewClass:function(e){return this.viewClass},_getItemViewOptions:function(e){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:a.contains(this.selected,e.id),draggable:this.dragItems}},_setUpItemViewListeners:function(e){var t=this;return this.listenTo(e,"all",function(){var e=Array.prototype.slice.call(arguments,0);e[0]="view:"+e[0],t.trigger.apply(t,e)}),this.listenTo(e,"draggable:dragstart",function(e,t){var i={},n=this.getSelectedModels();i=n.length?n.toJSON():[t.model.toJSON()],e.dataTransfer.setData("text",JSON.stringify(i))},this),t},_attachItems:function(e){var t=this;return this.$list(e).append(this.views.map(function(e){return t._renderItemView$el(e)})),this},_renderItemView$el:function(e){return e.render(0).$el},_renderEmptyMessage:function(e){this.debug("_renderEmptyMessage",e,this.searchFor);var t=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(e).text(t)},expandAll:function(){a.each(this.views,function(e){e.expand()})},collapseAll:function(){a.each(this.views,function(e){e.collapse()})},addItemView:function(e,t,i){var n=this,s=n._filterCollection().indexOf(e);if(s!==-1){var o=n._createItemView(e);return r(o).queue("fx",[function(e){n.$emptyMessage().is(":visible")?n.$emptyMessage().fadeOut(n.fxSpeed,e):e()},function(e){n._attachView(o,s),e()}]),o}},_attachView:function(e,t,i){i=!!a.isUndefined(i)||i,t=t||0;var n=this;return n.views.splice(t,0,e),n._insertIntoListAt(t,n._renderItemView$el(e).hide()),n.trigger("view:attached",e),i?e.$el.slideDown(n.fxSpeed,function(){n.trigger("view:attached:rendered")}):(e.$el.show(),n.trigger("view:attached:rendered")),e},_insertIntoListAt:function(e,t){var i=this.$list();return 0===e?i.prepend(t):i.children().eq(e-1).after(t),t},removeItemView:function(e,t,i){var n=this,s=a.find(n.views,function(t){return t.model===e});if(s)return n.views=a.without(n.views,s),n.trigger("view:removed",s),r({}).queue("fx",[function(e){s.$el.fadeOut(n.fxSpeed,e)},function(e){s.remove(),n.trigger("view:removed:rendered"),n.views.length?e():n._renderEmptyMessage().fadeIn(n.fxSpeed,e)}]),s},viewFromModelId:function(e){return a.find(this.views,function(t){return t.model.id===e})},viewFromModel:function(e){return e?this.viewFromModelId(e.id):void 0},viewsWhereModel:function(e){return this.views.filter(function(t){return a.isMatch(t.model.attributes,e)})},viewRange:function(e,t){if(e===t)return e?[e]:[];var i=this.views.indexOf(e),n=this.views.indexOf(t);return i===-1||n===-1?i===n?[]:i===-1?[t]:[e]:i .controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTOR_FX_AT:20,showSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,a.each(this.views,function(t){t.showSelector(e)})},hideSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,a.each(this.views,function(t){t.hideSelector(e)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(e){a.each(this.views,function(t){t.select(e)})},deselectAll:function(e){this.lastSelected=null,a.each(this.views,function(t){t.deselect(e)})},selectRange:function(e,t){var i=this.viewRange(e,t);return a.each(i,function(e){e.select()}),i},getSelectedViews:function(){return a.filter(this.views,function(e){return e.selected})},getSelectedModels:function(){return new this.collection.constructor(a.map(this.getSelectedViews(),function(e){return e.model}))},_showLoadingIndicator:function(e,i,n){this.debug("_showLoadingIndicator",this.indicator,e,i,n),i=void 0!==i?i:this.fxSpeed,this.indicator||(this.indicator=new t(this.$el),this.debug("\t created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(i),this.indicator.show(e,i,n)):this.indicator.show(0,n)},_hideLoadingIndicator:function(e,t){this.debug("_hideLoadingIndicator",this.indicator,e,t),e=void 0!==e?e:this.fxSpeed,this.indicator&&this.indicator.hide(e,t)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(e,t){return t=t||0,this.$scrollContainer().animate({scrollTop:e},t),this},scrollToTop:function(e){return this.scrollTo(0,e)},scrollToItem:function(e,t){return e?this:this},scrollToId:function(e,t){return this.scrollToItem(this.viewFromModelId(e),t)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});l.prototype.templates=function(){var e=i.wrapTemplate(["
    ",'
    ','
    ','
    ',"
    "]),t=i.wrapTemplate(['
    ','
    ','
    <%- view.title %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return{el:e,controls:t}}();var c=l.extend({modelCollectionKey:"contents",initialize:function(e){l.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting&&e.selecting,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=r(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});return c.prototype.templates=function(){var e=i.wrapTemplate(['
    ','
    ','
    <%- model.name %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
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            "].join("")),_showAjaxIndicator:function(){var e='
             '+this.progressive+"...
            ";this.modal.$(".modal-body").empty().append(e).css({"margin-top":"8px"})},dialog:function(e,n,s){function l(){var i=e.$("#copy-modal-title").val();if(!i)return void e.$(".invalid-title").show();var s="copy-all"===e.$('input[name="copy-what"]:checked').val();e.$("button").prop("disabled",!0),c._showAjaxIndicator(),n.copy(!0,i,s).done(function(e){d.resolve(e)}).fail(function(e,o,a){var r={name:i,copyAllDatasets:s};t.ajaxErrorModal(n,e,r,c.errorMessage),d.rejectWith(d,arguments)}).done(function(){f&&e.hide()})}s=s||{};var c=this,d=a.Deferred(),h=s.nameFn||this.defaultName,u=h({name:n.get("name")}),p=s.allDatasets?"copy-all":"copy-non-deleted",g=!!o.isUndefined(s.allowAll)||s.allowAll,f=!!o.isUndefined(s.autoClose)||s.autoClose;this.modal=e;var m=s.closing_callback;return e.show(o.extend(s,{title:this.title({name:n.get("name")}),body:r(c._template({name:u,isAnon:Galaxy.user.isAnonymous(),allowAll:g,copyWhat:p,activeLabel:this.activeLabel,allLabel:this.allLabel,anonWarning:this.anonWarning})),buttons:o.object([[i("Cancel"),function(){e.hide()}],[this.submitLabel,l]]),height:"auto",closing_events:!0,closing_callback:function(e){e&&d.reject({cancelled:!0}),m&&m(e)}})),e.$("#copy-modal-title").focus().select(),e.$("#copy-modal-title").on("keydown",function(e){13===e.keyCode&&(e.preventDefault(),l())}),d}},s=o.extend({},n,{defaultName:o.template("imported: <%- name %>"),title:o.template(i("Importing history")+' "<%- name %>"'),submitLabel:i("Import"),errorMessage:i("History could not be imported."),progressive:i("Importing history"),activeLabel:i("Import only the active, non-deleted datasets"),allLabel:i("Import all datasets including deleted ones"),anonWarning:i("As an anonymous user, unless you login or register, you will lose your current history ")+i("after importing this history. ")}),l=function(t,i){i=i||{};var o=window.parent.Galaxy.modal||new e.View({});return i.useImport?s.dialog(o,t,i):n.dialog(o,t,i)};return l}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(69),i(71),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=e.DatasetListItemEdit,r=s.extend({className:s.prototype.className+" history-content",_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):e.model.has("rerunnable")?o.when():e.model.fetch({silent:!0,data:{keys:["rerunnable","creating_job"].join(",")}})},events:a.extend(a.clone(s.prototype.events),{"click .unhide-link":function(e){return this.model.unhide(),!1}}),toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAListItemEdit("+e+")"}});return r.prototype.templates=function(){var e=a.extend({},s.prototype.templates.warnings,{hidden:i.wrapTemplate(["<% if( !dataset.visible ){ %>",'
            ',n("This dataset has been hidden"),'
            ',n("Unhide it"),"","
            ","<% } %>"],"dataset")});return a.extend({},s.prototype.templates,{titleBar:t.HDAListItemView.prototype.templates.titleBar,warnings:e})}(),{HDAListItemEdit:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;n=[i(73),i(108),i(22),i(5)],s=function(e,t,i,n){"use strict";var s=e.HDCAListItemView,o=s.extend({_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return t.ListCollectionViewEdit;case"paired":return t.PairCollectionViewEdit;case"list:paired":return t.ListOfPairsCollectionViewEdit;case"list:list":return t.ListOfListsCollectionViewEdit}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_renderPrimaryActions:function(){return this.log(this+"._renderPrimaryActions"),s.prototype._renderPrimaryActions.call(this).concat([this._renderDeleteButton()])},_renderDeleteButton:function(){var e=this,t=this.model.get("deleted");return i({title:n(t?"Dataset collection is already deleted":"Delete"),classes:"delete-btn",faIcon:"fa-times",disabled:t,onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDCAListItemEdit("+e+")"}});return{HDCAListItemEdit:o}}.apply(t,n),!(void 0!==s&&(e.exports=s));
 },function(e,t,i){var n,s;(function(o,a,r){n=[i(75),i(115),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=i.SessionStorageModel.extend({defaults:{tagsEditorShown:!1,annotationEditorShown:!1,scrollPosition:0},toString:function(){return"HistoryViewPrefs("+JSON.stringify(this.toJSON())+")"}});s.storageKey=function(){return"history-panel"};var l=t.HistoryViewEdit,c=l.extend({className:l.prototype.className+" current-history-panel",HDCAViewClass:l.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),emptyMsg:[n("This history is empty"),". ",n("You can "),'',n("load your own data"),"",n(" or "),'',n("get data from an external source"),""].join(""),initialize:function(e){e=e||{},this.preferences=new s(o.extend({id:s.storageKey()},o.pick(e,o.keys(s.prototype.defaults)))),l.prototype.initialize.call(this,e),this.panelStack=[],this.currentContentId=e.currentContentId||null},_setUpListeners:function(){l.prototype._setUpListeners.call(this);var e=this;this.on("new-model",function(){e.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(){return this.loadHistory(null,{url:Galaxy.root+"history/current_history_json"})},switchToHistory:function(e,t){return Galaxy.user.isAnonymous()?(this.trigger("error",n("You must be logged in to switch histories"),n("Anonymous user")),a.when()):this.loadHistory(e,{url:Galaxy.root+"history/set_as_current?id="+e})},createNewHistory:function(e){return Galaxy.user.isAnonymous()?(this.trigger("error",n("You must be logged in to create histories"),n("Anonymous user")),a.when()):this.loadHistory(null,{url:Galaxy.root+"history/create_new_current"})},setModel:function(e,t,i){return l.prototype.setModel.call(this,e,t,i),this.model&&this.model.id&&(this.log("checking for updates"),this.model.checkForUpdates()),this},_setUpModelListeners:function(){return l.prototype._setUpModelListeners.call(this),this.listenTo(this.model,{"change:nice_size change:size":function(){this.trigger("history-size-change",this,this.model,arguments)},"change:id":function(){this.once("loading-done",function(){this.model.checkForUpdates()})}})},_setUpCollectionListeners:function(){l.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,"state:ready",function(e,t,i){e.get("visible")||this.collection.storage.includeHidden()||this.removeItemView(e)})},_setUpBehaviors:function(e){e=e||this.$el;var t=this;return l.prototype._setUpBehaviors.call(t,e),this._debouncedScrollCaptureHandler||(this._debouncedScrollCaptureHandler=o.debounce(function(){t.$el.is(":visible")&&t.preferences.set("scrollPosition",a(this).scrollTop())},40)),t.$scrollContainer(e).off("scroll",this._debouncedScrollCaptureHandler).on("scroll",this._debouncedScrollCaptureHandler),t},_buildNewRender:function(){if(!this.model)return a();var e=l.prototype._buildNewRender.call(this);return e.find(".search").prependTo(e.find("> .controls")),this._renderQuotaMessage(e),e},_renderQuotaMessage:function(e){return e=e||this.$el,a(this.templates.quotaMsg({},this)).prependTo(e.find(".messages"))},_renderTags:function(e){var t=this;l.prototype._renderTags.call(t,e),t.preferences.get("tagsEditorShown")&&t.tagsEditor.toggle(!0),t.listenTo(t.tagsEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("tagsEditorShown",e.hidden)})},_renderAnnotation:function(e){var t=this;l.prototype._renderAnnotation.call(t,e),t.preferences.get("annotationEditorShown")&&t.annotationEditor.toggle(!0),t.listenTo(t.annotationEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("annotationEditorShown",e.hidden)})},_swapNewRender:function(e){l.prototype._swapNewRender.call(this,e);var t=this;return o.delay(function(){var e=t.preferences.get("scrollPosition");e&&t.scrollTo(e,0)},10),this},_attachItems:function(e){l.prototype._attachItems.call(this,e);var t=this;return t.currentContentId&&t._setCurrentContentById(t.currentContentId),this},addItemView:function(e,t,i){var n=l.prototype.addItemView.call(this,e,t,i);return n&&this.panelStack.length?this._collapseDrilldownPanel():n},_setUpItemViewListeners:function(e){var t=this;return l.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}})},setCurrentContent:function(e){this.$(".history-content.current-content").removeClass("current-content"),e?(e.$el.addClass("current-content"),this.currentContentId=e.model.id):this.currentContentId=null},_setCurrentContentById:function(e){var t=this.viewFromModelId(e)||null;this.setCurrentContent(t)},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$controls().add(this.$list()).hide(),e.parentName=this.model.get("name"),e.delegateEvents().render().$el.appendTo(this.$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.$controls().add(this.$list()).show()},events:o.extend(o.clone(l.prototype.events),{"click .uploader-link":function(e){Galaxy.upload.show(e)},"click .get-data-link":function(e){var t=a(".toolMenuContainer");t.parent().scrollTop(0),t.find('span:contains("Get Data")').click()}}),listenToGalaxy:function(e){this.listenTo(e,{"galaxy_main:load":function(e){var t=e.fullpath,i=null,n={display:/datasets\/([a-f0-9]+)\/display/,edit:/datasets\/([a-f0-9]+)\/edit/,report_error:/dataset\/errors\?id=([a-f0-9]+)/,rerun:/tool_runner\/rerun\?id=([a-f0-9]+)/,show_params:/datasets\/([a-f0-9]+)\/show_params/};o.find(n,function(e,n){return i=o.result(t.match(e),1)}),this._setCurrentContentById(i?"dataset-"+i:null)},"center-panel:load":function(e){this._setCurrentContentById()}})},connectToQuotaMeter:function(e){return e?(this.listenTo(e,"quota:over",this.showQuotaMessage),this.listenTo(e,"quota:under",this.hideQuotaMessage),this.on("rendered rendered:initial",function(){e&&e.isOverQuota()&&this.showQuotaMessage()}),this):this},clearMessages:function(e){var t=o.isUndefined(e)?this.$messages().children('[class$="message"]'):a(e.currentTarget);return t=t.not(".quota-message"),t.fadeOut(this.fxSpeed,function(){a(this).remove()}),this},showQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")&&e.slideDown(this.fxSpeed)},hideQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")||e.slideUp(this.fxSpeed)},unhideHidden:function(){var e=this;return confirm(n("Really unhide all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{visible:!0}).done(function(){e.model.contents.includeHidden||e.renderItems()}):r.when()},deleteHidden:function(){var e=this;return confirm(n("Really delete all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{deleted:!0,visible:!0}):r.when()},toString:function(){return"CurrentHistoryView("+(this.model?this.model.get("name"):"")+")"}});return c.prototype.templates=function(){var e=i.wrapTemplate(['
            ',n("You are over your disk quota"),". ",n("Tool execution is on hold until your disk usage drops below your allocated quota"),".","
            "],"history");return o.extend(o.clone(l.prototype.templates),{quotaMsg:e})}(),{CurrentHistoryView:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(116),i(41),i(12),i(72),i(112),i(113),i(77),i(66),i(33),i(110),i(109),i(22),i(80),i(6),i(5),i(15)],s=function(e,t,i,n,s,l,c,d,h,u,p,g,f,m,v){"use strict";var _=e.HistoryView,y=_.extend({HDAViewClass:s.HDAListItemEdit,HDCAViewClass:l.HDCAListItemEdit,initialize:function(e){e=e||{},_.prototype.initialize.call(this,e),this.tagsEditor=null,this.annotationEditor=null,this.purgeAllowed=e.purgeAllowed||!1,this.annotationEditorShown=e.annotationEditorShown||!1,this.tagsEditorShown=e.tagsEditorShown||!1},_setUpListeners:function(){return _.prototype._setUpListeners.call(this),this.on({"droptarget:drop":function(e,t){this.dataDropped(t),this.dropTargetOff()},"view:attached view:removed":function(){this._renderCounts()},"search:loading-progress":this._renderSearchProgress,"search:searching":this._renderSearchFindings})},_setUpModelListeners:function(){return _.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_setUpCollectionListeners:function(){return _.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleItemDeletedChange,"change:visible":this._handleItemVisibleChange,"change:purged":function(e){this.model.fetch()},"fetching-deleted":function(e){this.$("> .controls .deleted-count").html(""+v("loading...")+"")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html(""+v("loading...")+"")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=_.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".history-size").text(this.model.get("nice_size"))},renderItems:function(e){var t=_.prototype.renderItems.call(this,e);return this.searchFor||this._renderCounts(e),t},_renderCounts:function(e){e=e instanceof o?e:this.$el;var t=this.templates.counts(this.model.toJSON(),this);return e.find("> .controls .subtitle").html(t)},_renderTags:function(e){var t=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:e.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDATagEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDATagEditors(!1,t.fxSpeed)},$activator:g({title:v("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:g({title:v("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,_.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this,i="> .controls .name";e.find(i).attr("title",v("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var n=t.model.get("name");e&&e!==n?(t.$el.find(i).text(e),t.model.save({name:e}).fail(function(){t.$el.find(i).text(t.model.previous("name"))})):t.$el.find(i).text(n)}})}},multiselectActions:function(){var e=this,t=[{html:v("Hide datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:v("Unhide datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:v("Delete datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:v("Undelete datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:v("Permanently delete datasets"),func:function(){if(confirm(v("This will permanently remove the data in your datasets. Are you sure?"))){var t=n.HistoryDatasetAssociation.prototype.purge;e.getSelectedModels().ajaxQueue(t)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:v("Build Dataset List"),func:function(){h.createListCollection(e.getSelectedModels()).done(function(){e.model.refresh()})}},{html:v("Build Dataset Pair"),func:function(){u.createPairCollection(e.getSelectedModels()).done(function(){e.model.refresh()})}},{html:v("Build List of Dataset Pairs"),func:function(){p.createListOfPairsCollection(e.getSelectedModels()).done(function(){e.model.refresh()})}}]},_getItemViewOptions:function(e){var t=_.prototype._getItemViewOptions.call(this,e);return a.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){a.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){a.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:a.extend(a.clone(_.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["",v("Searching "),i,"/",this.model.contentsShown(),""].join(""))},_renderSearchFindings:function(){return this.$("> .controls .subtitle").html([v("Found"),this.views.length].join(" ")),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:a.bind(this.dragenter,this),dragover:a.bind(this.dragover,this),dragleave:a.bind(this.dragleave,this),drop:a.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),r("
            ").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),r("
            ").addClass("history-drop-target-help").text(v("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".history-drop-target").get(0);for(var t in this._dropHandlers)this._dropHandlers.hasOwnProperty(t)&&e.off(t,this._dropHandlers[t]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(e){e.preventDefault(),e.stopPropagation()},dragleave:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(e){e.preventDefault();var t=this,i=e.originalEvent.dataTransfer,n=i.getData("text");i.dropEffect="move";try{n=JSON.parse(n)}catch(e){t.warn("error parsing JSON from drop:",n)}return t.trigger("droptarget:drop",e,n,t),!1},dataDropped:function(e){var t=this;return a.isObject(e)&&"HistoryDatasetAssociation"===e.model_class&&e.id?0!==t.contents.currentPage?t.contents.fetchPage(0).then(function(){return t.model.contents.copy(e.id)}):t.model.contents.copy(e.id):o.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});return y.prototype.templates=function(){var e=m.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'',"<%- shown %> ",v("shown"),"","<% } %>","<% if( history.contents_active.deleted ){ %>",'',"<% if( view.model.contents.includeDeleted ){ %>",'',v("hide deleted"),"","<% } else { %>","<%- history.contents_active.deleted %> ",'',v("deleted"),"","<% } %>","","<% } %>","<% if( history.contents_active.hidden ){ %>",'',"<% if( view.model.contents.includeHidden ){ %>",'',v("hide hidden"),"","<% } else { %>","<%- history.contents_active.hidden %> ",'',v("hidden"),"","<% } %>","","<% } %>"],"history");return a.extend(a.clone(_.prototype.templates),{counts:e})}(),{HistoryViewEdit:y}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(76),i(75),i(41),i(42),i(71),i(73),i(83),i(79),i(22),i(6),i(5),i(86)],s=function(e,t,i,n,s,r,l,c,d,h,u){"use strict";var p=e.ModelListPanel,g=p.extend({_logNamespace:"history",HDAViewClass:s.HDAListItemView,HDCAViewClass:r.HDCAListItemView,collectionClass:i.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:p.prototype.className+" history-panel",emptyMsg:u("This history is empty"),noneFoundMsg:u("No matching datasets found"),searchPlaceholder:u("search datasets"),FETCH_COLLECTION_COUNTS_DELAY:2e3,initialize:function(e){p.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_createDefaultCollection:function(){return new this.collectionClass([],{history:this.model})},freeModel:function(){return p.prototype.freeModel.call(this),this.model&&this.model.clearUpdateTimeout(),this},_setUpListeners:function(){p.prototype._setUpListeners.call(this),this.on({error:function(e,t,i,n,s){this.errorHandler(e,t,i,n,s)},"loading-done":function(){var e=this;o.delay(function(){e.model.contents.fetchCollectionCounts()},e.FETCH_COLLECTION_COUNTS_DELAY)},"views:ready view:attached view:removed":function(e){this._renderSelectButton()},"view:attached":function(e){this.scrollTo(0)}})},loadHistory:function(e,i,n){n=o.extend(n||{silent:!0}),this.info("loadHistory:",e,i,n);var s=this;return s.setModel(new t.History({id:e})),n.silent=!0,s.trigger("loading"),s.model.fetchWithContents(i,n).always(function(){s.render(),s.trigger("loading-done")})},refreshContents:function(e){return this.model?this.model.refresh(e):a.when()},_setUpCollectionListeners:function(){return p.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"fetching-more":function(){this._toggleContentsLoadingIndicator(!0),this.$emptyMessage().hide()},"fetching-more-done":function(){this._toggleContentsLoadingIndicator(!1)}})},_showLoadingIndicator:function(e,t,i){var n=a('
            ');this.$el.html(n.text(e).slideDown(o.isUndefined(t)?this.fxSpeed:t))},_hideLoadingIndicator:function(e){this.$(".loading-indicator").slideUp(o.isUndefined(e)?this.fxSpeed+200:e,function(){a(this).remove()})},_buildNewRender:function(){var e=p.prototype._buildNewRender.call(this);return this._renderSelectButton(e),e},_renderSelectButton:function(e){if(e=e||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:d({title:u("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"}).prependTo(e.find(".controls .actions"))},_renderEmptyMessage:function(e){var t=this,i=t.$emptyMessage(e),n=t.model.get("contents_active").active<=0;return n?i.empty().append(t.emptyMsg).show():t.searchFor&&t.model.contents.haveSearchDetails()&&!t.views.length?i.empty().append(t.noneFoundMsg).show():(i.hide(),a())},$scrollContainer:function(e){return this.$list(e)},_toggleContentsLoadingIndicator:function(e){e?this.$list().html('
            '):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this,i=t.$list(e);a(".tooltip").remove(),i.empty(),t.views=[];var n=t._filterCollection();return n.length?(t._renderPagination(e),t.views=t._renderSomeItems(n,i)):e.find("> .controls .list-pagination").empty(),t._renderEmptyMessage(e).toggle(!n.length),t.trigger("views:ready",t.views),t.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var i=this,n=[];return t.append(e.map(function(e){var t=i._createItemView(e);return n.push(t),i._renderItemView$el(t)})),n},_filterItem:function(e){var t=this,i=t.model.contents;return(i.includeHidden||!e.hidden())&&(i.includeDeleted||!e.isDeletedOrPurged())&&p.prototype._filterItem.call(t,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(e){var t=p.prototype._getItemViewOptions.call(this,e);return o.extend(t,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(e.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),p.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=p.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:o.extend(o.clone(p.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.clearUpdateTimeout(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.clearUpdateTimeout(),this.model.contents.fetchNextPage()},_changePageSelect:function(e){this.model.clearUpdateTimeout();var t=a(e.currentTarget).val();this.model.contents.fetchPage(t)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var i=this,n=i.model.contents;return n.setIncludeDeleted(e,t),i.trigger("show-deleted",e),n.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,i){e=void 0!==e?e:!this.model.contents.includeHidden;var n=this,s=n.model.contents;return s.setIncludeHidden(e,i),n.trigger("show-hidden",e),s.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this,i="> .controls .search-input";if(this.log("onFirstSearch",e),t.model.contents.haveSearchDetails())return void t.searchItems(e);t.$(i).searchInput("toggle-loading"),t.searchFor=e;t.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,i,n){t.renderItems(),t.trigger("search:loading-progress",i,n)}).always(function(){t.$el.find(i).searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})},clearSearch:function(e){var t=this;return t.searchFor?(t.searchFor="",t.trigger("search:clear",t),t.$("> .controls .search-query").val(""),t.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),t):t},errorHandler:function(e,t,i){if(!t||0!==t.status||0!==t.readyState){if(this.error(e,t,i),o.isString(e)&&o.isString(t)){var n=e,s=t;return c.errorModal(n,s,i)}return t&&502===t.status?c.badGatewayErrorModal():c.ajaxErrorModal(e,t,i)}},clearMessages:function(e){var t=o.isUndefined(e)?this.$messages().children('[class$="message"]'):a(e.currentTarget);return t.fadeOut(this.fxSpeed,function(){a(this).remove()}),this},scrollToHid:function(e){return this.scrollToItem(o.first(this.viewsWhereModel({hid:e})))},ordinalIndicator:function(e){var t=e+"";switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});return g.prototype.templates=function(){var e=h.wrapTemplate(["
            ",'
            ','
              ','
              ',"
              "]),t=h.wrapTemplate(['
              ','
              ','
              <%- history.name %>
              ',"
              ",'
              ','
              <%- history.nice_size %>
              ','
              ','
              ',"<% if( history.deleted && history.purged ){ %>",'
              ',u("This history has been purged and deleted"),"
              ","<% } else if( history.deleted ){ %>",'
              ',u("This history has been deleted"),"
              ","<% } else if( history.purged ){ %>",'
              ',u("This history has been purged"),"
              ","<% } %>","<% if( history.message ){ %>",'
              messagesmall">',"<%= history.message.text %>","
              ","<% } %>","
              ",'
              ','
              ','
              ','
              ',"
              ",'
              ','
              ','",'","
              ",'
              ',"
              ","
              ",'
              ',"
              "],"history"),i=h.wrapTemplate(['','",''],"pages");return o.extend(o.clone(p.prototype.templates),{el:e,controls:t,pagination:i})}(),{HistoryView:g}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(80),i(111),i(6),i(5),i(27)],s=function(e,t,i,n,s){"use strict";function r(e,t,i){return a.clone(l).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target="galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}var l=[{html:n("History Lists"),header:!0},{html:n("Saved Histories"),href:"history/list"},{html:n("Histories Shared with Me"),href:"history/list_shared"},{html:n("Current History"),header:!0,anon:!0},{html:n("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:n("Copy History"),func:function(){t(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Share or Publish"),href:"history/sharing"},{html:n("Show Structure"),href:"history/display_structured",anon:!0},{html:n("Extract Workflow"),href:"workflow/build_from_current_history"},{html:n("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:n("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:n("Dataset Actions"),header:!0,anon:!0},{html:n("Copy Datasets"),href:"dataset/copy_datasets"},{html:n("Dataset Security"),href:"root/history_set_default_permissions"},{html:n("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:n("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:n("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really unhide all hidden datasets?"))&&o.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete all hidden datasets?"))&&o.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Purge Deleted Datasets"),confirm:n("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:n("Downloads"),header:!0},{html:n("Export Tool Citations"),href:"history/citations",anon:!0},{html:n("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:n("Other Actions"),header:!0},{html:n("Import from File"),href:"history/import_archive"}];s.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(e){var t=[];o.each(e.models,function(e,i){var s=i.toJSON();s.activate&&t.push({html:n(s.config.title),anon:!0})}),t.length>0&&(t.unshift({html:n("Webhooks"),header:!0}),o.merge(l,t))}});var c=function(t,i){i=i||{};var n=void 0===i.anonymous||i.anonymous,s=i.purgeAllowed||!1,o=r(n,s,Galaxy.root);return new e(t,o)};return c}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(4)],s=function(e){var t=o.View.extend({initialize:function(e){this.collection=new o.Collection,this.model=e&&e.model||new o.Model({onchange:null,visible:!0}).set(e),this.setElement(a(this._template())),this.$nav=this.$(".tab-navigation"),this.$content=this.$(".tab-content"),this.$el.on("click",function(){a(".tooltip").hide()}),this.render(),this.listenTo(this.model,"change",this.render,this),this.listenTo(this.collection,"add",this._add,this),this.listenTo(this.collection,"remove",this._remove,this),this.listenTo(this.collection,"change",this._change,this),this.listenTo(this.collection,"reset",this._reset,this),this.listenTo(this.collection,"add remove reset",this.render,this)},render:function(){var e=this.model.get("current");e=this.$("#"+e).length>0?e:this.first(),e&&(this.$nav.children().removeClass("active"),this.$content.children().removeClass("active"),this.$("#tab-"+e).addClass("active"),this.$("#"+e).addClass("active")),this.$el[this.model.get("visible")?"fadeIn":"fadeOut"]("fast"),this.$nav[this.size()>1?"show":"hide"]()},current:function(){return this.model.get("current")},show:function(e){e&&(this.model.set({current:e,visible:!0}),this.model.get("onchange")&&this.model.get("onchange")(e))},hide:function(){this.model.set("visible",!1)},first:function(){var e=this.collection.first();return e&&e.id},size:function(){return this.collection.length;
 },add:function(e){this.collection.add(e)},del:function(e){this.collection.remove(e)},delAll:function(){this.collection.reset()},showTab:function(e){this.collection.get(e).set("hidden",!1)},hideTab:function(e){this.collection.get(e).set("hidden",!0)},_add:function(e){var t=this,i=e.attributes;this.$content.append(a("
              ").attr("id",i.id).addClass("tab-pane").append(i.$el)),this.$nav.append(a(this._template_tab(i)).show().tooltip({title:i.tooltip,placement:"bottom",container:t.$el}).on("click",function(e){e.preventDefault(),t.show(i.id)})),1==this.size()&&this.show(i.id)},_remove:function(e){this.$("#tab-"+e.id).remove(),this.$("#"+e.id).remove()},_reset:function(){this.$nav.empty(),this.$content.empty()},_change:function(e){this.$("#tab-"+e.id)[e.get("hidden")?"hide":"show"]()},_template:function(){return a("
              ").addClass("ui-tabs tabbable tabs-left").append(a("