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Galaxy Tours
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Galaxy Tours
\n
This page presents a list of interactive tours available on this Galaxy server.\n Select any tour to get started (and remember, you can click \'End Tour\' at any time).
This page presents a list of interactive tours available on this Galaxy server.\n Select any tour to get started (and remember, you can click \'End Tour\' at any time).
\n<% }); %>'),e={};c.each(this.model.models,function(t){null===t.attributes.tags?(void 0===e.Untagged&&(e.Untagged={name:"Untagged",tours:[]}),e.Untagged.tours.push(t)):c.each(t.attributes.tags,function(n){n=n.charAt(0).toUpperCase()+n.slice(1),void 0===e[n]&&(e[n]={name:n,tours:[]}),e[n].tours.push(t)})});var n=Object.keys(e).sort();this.$el.html(t({tours:this.model.models,tourtags:e,tourtagorder:n})).on("click",".tourItem",function(t){t.preventDefault(),i($(this).data("tour.id"))}).on("click",".tag-selector-button",function(t){var e=$(t.target),n="block",o=e.attr("tag-selector-button");e.toggleClass("btn-primary"),e.toggleClass("btn-secondary"),e.hasClass("btn-secondary")&&(n="none"),$("div[tag='"+o+"']").css({display:n})})}});t.default={ToursView:b,giveTourWithData:r,giveTourById:i,activeGalaxyTourRunner:s}});
\ No newline at end of file
+define("mvc/tours",["exports","utils/localization","libs/backbone","libs/underscore","libs/bootstrap-tour"],function(t,e,n,o){"use strict";function a(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}function r(t){var e=f(t);window.sessionStorage.setItem("activeGalaxyTour",JSON.stringify(t));var n=new d(c.extend({steps:e.steps},p));return n.init(),n.goTo(0),n.restart(),n}function i(t){var e=g+"api/tours/"+t;$.getJSON(e,function(t){r(t)})}function s(){var t=JSON.parse(window.sessionStorage.getItem("activeGalaxyTour"));if(t&&(t=f(t))&&t.steps&&window&&window.self===window.top){var e=new d(c.extend({steps:t.steps},p));e.init(),e.restart()}}Object.defineProperty(t,"__esModule",{value:!0}),t.ToursView=void 0,t.giveTourWithData=r,t.giveTourById=i,t.activeGalaxyTourRunner=s;var u=function(t){return t&&t.__esModule?t:{default:t}}(e),l=a(n),c=a(o),d=window.Tour,g="undefined"==typeof Galaxy?"/":Galaxy.root,p={storage:window.sessionStorage,onEnd:function(){window.sessionStorage.removeItem("activeGalaxyTour")},delay:150,orphan:!0},f=function(t){return c.each(t.steps,function(t){t.preclick&&(t.onShow=function(){c.each(t.preclick,function(t){$(t).click()})}),t.postclick&&(t.onHide=function(){c.each(t.postclick,function(t){$(t).click()})}),t.textinsert&&(t.onShown=function(){$(t.element).val(t.textinsert).trigger("change")}),t.path&&(console.warn("This Galaxy Tour is attempting to use path navigation. This is known to be unstable and can possibly get the Galaxy client 'stuck' in a tour, and at this time is not allowed."),delete t.path)}),t},h=l.Model.extend({urlRoot:g+"api/tours"}),v=l.Collection.extend({url:g+"api/tours",model:h}),b=t.ToursView=l.View.extend({title:(0,u.default)("Tours"),initialize:function(){var t=this;this.setElement(""),this.model=new v,this.model.fetch({success:function(){t.render()},error:function(){console.error("Failed to fetch tours.")}})},render:function(){var t=c.template('\n
Galaxy Tours
\n
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Galaxy Tours
\n
This page presents a list of interactive tours available on this Galaxy server.\n Select any tour to get started (and remember, you can click \'End Tour\' at any time).
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Galaxy Tours
\n
This page presents a list of interactive tours available on this Galaxy server.\n Select any tour to get started (and remember, you can click \'End Tour\' at any time).
This page presents a list of interactive tours available on this Galaxy server.\n Select any tour to get started (and remember, you can click \'End Tour\' at any time).
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\ No newline at end of file
+define("mvc/tours",["exports","utils/localization","libs/backbone","libs/underscore","libs/bootstrap-tour"],function(t,e,n,o){"use strict";function a(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}function r(t){var e=f(t);window.sessionStorage.setItem("activeGalaxyTour",JSON.stringify(t));var n=new d(c.extend({steps:e.steps},p));return n.init(),n.goTo(0),n.restart(),n}function i(t){var e=g+"api/tours/"+t;$.getJSON(e,function(t){r(t)})}function s(){var t=JSON.parse(window.sessionStorage.getItem("activeGalaxyTour"));if(t&&(t=f(t))&&t.steps&&window&&window.self===window.top){var e=new d(c.extend({steps:t.steps},p));e.init(),e.restart()}}Object.defineProperty(t,"__esModule",{value:!0}),t.ToursView=void 0,t.giveTourWithData=r,t.giveTourById=i,t.activeGalaxyTourRunner=s;var u=function(t){return t&&t.__esModule?t:{default:t}}(e),l=a(n),c=a(o),d=window.Tour,g="undefined"==typeof Galaxy?"/":Galaxy.root,p={storage:window.sessionStorage,onEnd:function(){window.sessionStorage.removeItem("activeGalaxyTour")},delay:150,orphan:!0},f=function(t){return c.each(t.steps,function(t){t.preclick&&(t.onShow=function(){c.each(t.preclick,function(t){$(t).click()})}),t.postclick&&(t.onHide=function(){c.each(t.postclick,function(t){$(t).click()})}),t.textinsert&&(t.onShown=function(){$(t.element).val(t.textinsert).trigger("change")}),t.path&&(console.warn("This Galaxy Tour is attempting to use path navigation. This is known to be unstable and can possibly get the Galaxy client 'stuck' in a tour, and at this time is not allowed."),delete t.path)}),t},h=l.Model.extend({urlRoot:g+"api/tours"}),v=l.Collection.extend({url:g+"api/tours",model:h}),b=t.ToursView=l.View.extend({title:(0,u.default)("Tours"),initialize:function(){var t=this;this.setElement(""),this.model=new v,this.model.fetch({success:function(){t.render()},error:function(){console.error("Failed to fetch tours.")}})},render:function(){var t=c.template('\n
Galaxy Tours
\n
This page presents a list of interactive tours available on this Galaxy server.\n Select any tour to get started (and remember, you can click \'End Tour\' at any time).
`);
} else {
return this._templateError(response, "Invalid success response. No invocations found.");
}
From 87dc52cd8fedf64e895d0aa8421207f52a390e01 Mon Sep 17 00:00:00 2001
From: Dannon Baker
Date: Thu, 31 May 2018 19:47:03 -0400
Subject: [PATCH 16/24] Only show 'switch to this history' when the person in
question is the history owner.
---
client/galaxy/scripts/components/HistoryView.vue | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/client/galaxy/scripts/components/HistoryView.vue b/client/galaxy/scripts/components/HistoryView.vue
index 77079b2f5ef..999632663fd 100644
--- a/client/galaxy/scripts/components/HistoryView.vue
+++ b/client/galaxy/scripts/components/HistoryView.vue
@@ -6,7 +6,7 @@
-
+
From 5a0f98802cab73dfcdaef01b1200e96bc6b9a8ae Mon Sep 17 00:00:00 2001
From: Nicola Soranzo
Date: Wed, 6 Jun 2018 12:22:24 +0100
Subject: [PATCH 17/24] Strip a spurious Slurm warning from job stderr
Reason for the Slurm warning
----------------------------
The Linux kernel memory controller (responsible for the memory cgroup) may
run out of cgroup subsystem state (CSS) IDs. When a cgroup is created it is
assigned a CSS ID to manage its state. Upon removal of the cgroup the
corresponding state information (e.g. cache entries) may still exist and
therefore the CSS ID is still held. When multiple frequent short-lived jobs
are run on a cluster node, the number of available CSS IDs becomes exhausted
and creating a new memory cgroup results in a ENOSPC ("No space left on
device"), which is reported by SLURM with the message "unable to add
task[pid=] to memory cg '(null)'" (even if jobs run fine).
There is a bugfix for the kernel that releases the CSS ID upon cgroup
destruction, but it appears to be only available after Linux 4.4. We use
CentOS 7, which is based on Linux 3.10. The only temporary solutions is to
reboot the affected cluster node.
Thanks to @tuxtobin for the detailed analysis above.
Reason for this patch
---------------------
Many tools rely on an empty stderr to determine if the job was successful,
either because they were never updated to use ``/`detect_errors`, or
because the underlying tool returns a non-zero exit code when successful,
e.g. `tranalign` from
https://toolshed.g2.bx.psu.edu/view/devteam/emboss_5/832c20329690 .
Even using a `` inside `` would not work because the Slurm
warning contains the word `error`.
---
lib/galaxy/jobs/runners/slurm.py | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/lib/galaxy/jobs/runners/slurm.py b/lib/galaxy/jobs/runners/slurm.py
index c4c38163f9a..5c7856f1dfc 100644
--- a/lib/galaxy/jobs/runners/slurm.py
+++ b/lib/galaxy/jobs/runners/slurm.py
@@ -3,7 +3,10 @@ SLURM job control via the DRMAA API.
"""
import logging
import os
+import re
+import shutil
import subprocess
+import tempfile
import time
from galaxy import model
@@ -25,6 +28,7 @@ SLURM_MEMORY_LIMIT_EXCEEDED_MSG = 'slurmstepd: error: Exceeded job memory limit'
SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS = [': Exceeded job memory limit at some point.',
': Exceeded step memory limit at some point.']
SLURM_MEMORY_LIMIT_SCAN_SIZE = 16 * 1024 * 1024 # 16MB
+SLURM_UNABLE_TO_ADD_TASK_TO_MEMORY_CG_MSG_RE = re.compile(r"""slurmstepd: error: task/cgroup: unable to add task\[pid=\d+\] to memory cg '\(null\)'$""")
# These messages are returned to the user
OUT_OF_MEMORY_MSG = 'This job was terminated because it used more memory than it was allocated.'
@@ -149,6 +153,14 @@ class SlurmJobRunner(DRMAAJobRunner):
self.work_queue.put((self.fail_job, ajs))
return
if drmaa_state == self.drmaa_job_states.DONE:
+ with open(ajs.error_file, 'r') as rfh:
+ first_line = rfh.readline()
+ if SLURM_UNABLE_TO_ADD_TASK_TO_MEMORY_CG_MSG_RE.match(first_line):
+ with tempfile.NamedTemporaryFile('w', delete=False) as wfh:
+ shutil.copyfileobj(rfh, wfh)
+ wf_name = wfh.name
+ shutil.move(wf_name, ajs.error_file)
+ log.debug('(%s/%s) Job completed, removing SLURM spurious warning: "%s"', ajs.job_wrapper.get_id_tag(), ajs.job_id, first_line)
with open(ajs.error_file, 'r+') as f:
if os.path.getsize(ajs.error_file) > SLURM_MEMORY_LIMIT_SCAN_SIZE:
f.seek(-SLURM_MEMORY_LIMIT_SCAN_SIZE, os.SEEK_END)
From ed56454ca07f3e07ce2bfced8614ca3dc560649a Mon Sep 17 00:00:00 2001
From: Martin Cech
Date: Thu, 7 Jun 2018 09:15:47 -0400
Subject: [PATCH 18/24] add the canonical url to grt config
---
scripts/grt/grt.yml.sample | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/scripts/grt/grt.yml.sample b/scripts/grt/grt.yml.sample
index ff67c01f9e6..8c9456f11ce 100644
--- a/scripts/grt/grt.yml.sample
+++ b/scripts/grt/grt.yml.sample
@@ -1,11 +1,13 @@
grt:
- # Go to https://telescope.galaxyproject.org to obtain an Instance ID and API key
+ # Register at https://telescope.galaxyproject.org to obtain an Instance ID and API key
instance_id:
api_key:
+
# Galaxy Project offers a public galactic-radio-telescope instance, however
# you are free to run your own if you need. We would love it if you were
# willing and able to contribute your data publicly.
- url: http://localhost:8080
+ url: https://telescope.galaxyproject.org/grt-admin/
+
# Are you willing to share your toolbox? I.e. what tools are installed.
# If your instance is public, this can help us direct users to your
# instance. If you elect to not send your entire toolbox, we will still
From 753ecd625c1410a3a6dc2c4a30e3f81fb71be29e Mon Sep 17 00:00:00 2001
From: mvdbeek
Date: Fri, 8 Jun 2018 09:52:58 +0200
Subject: [PATCH 19/24] Increase sleep if encountering exception
---
lib/galaxy/jobs/handler.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py
index de5eb4f4433..e92bad164ef 100644
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -213,6 +213,9 @@ class JobHandlerQueue(Monitors):
self.__monitor_step()
except Exception:
log.exception("Exception in monitor_step")
+ # With sqlite backends we can run into locked databases occasionally
+ # To avoid that the monitor step locks again we backoff a little longer.
+ self._monitor_sleep(5)
self._monitor_sleep(1)
def __monitor_step(self):
From 54ec854c130f92f49d2c3f42e2e8971d6676a79a Mon Sep 17 00:00:00 2001
From: Martin Cech
Date: Fri, 8 Jun 2018 13:19:13 -0400
Subject: [PATCH 20/24] remove outdated comment
---
client/galaxy/scripts/mvc/history/history-contents.js | 2 --
1 file changed, 2 deletions(-)
diff --git a/client/galaxy/scripts/mvc/history/history-contents.js b/client/galaxy/scripts/mvc/history/history-contents.js
index a57c28cef16..65052d2c667 100644
--- a/client/galaxy/scripts/mvc/history/history-contents.js
+++ b/client/galaxy/scripts/mvc/history/history-contents.js
@@ -35,8 +35,6 @@ var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
/** @type {String} order used here and when fetching from server */
order: "hid",
- /** root api url */
-
/** complete api url */
url: function() {
return `${this.urlRoot}/${this.historyId}/contents`;
From 7eb927b631a3677a74b055fc275b90827bcdff21 Mon Sep 17 00:00:00 2001
From: John Chilton
Date: Tue, 5 Jun 2018 15:27:31 -0400
Subject: [PATCH 21/24] Fix delete "Collection Only" option in history menu.
Broken with https://github.com/galaxyproject/galaxy/commit/7cc01380afd017c5cac2af2b2d735b2265774a68.
---
client/galaxy/scripts/mvc/history/hdca-li-edit.js | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/client/galaxy/scripts/mvc/history/hdca-li-edit.js b/client/galaxy/scripts/mvc/history/hdca-li-edit.js
index 3529063051a..a95f0554dd4 100644
--- a/client/galaxy/scripts/mvc/history/hdca-li-edit.js
+++ b/client/galaxy/scripts/mvc/history/hdca-li-edit.js
@@ -41,7 +41,7 @@ var HDCAListItemEdit = _super.extend(
","<% }); %>"],"apps");return e.extend({},g.prototype.templates,{warnings:t,details:i,noAccess:n,summaries:a,detailMessages:s,displayApplications:o})}(),t.default={DatasetListItemView:v}}).call(t,i(1),i(0),i(2),i(0))},,function(e,t,i){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}function a(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}Object.defineProperty(t,"__esModule",{value:!0});var s=i(1),o=(a(s),i(2)),r=a(o),l=i(6),d=n(l),c=i(3),u=n(c),h=r.Model.extend(d.default.LoggableMixin).extend({_logNamespace:"user",urlRoot:function(){return Galaxy.root+"api/users"},defaults:{id:null,username:"("+(0,u.default)("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null,is_admin:!1},initialize:function(e){this.log("User.initialize:",e),this.on("loaded",function(e,t){this.log(this+" has loaded:",e,t)}),this.on("change",function(e,t){this.log(this+" has changed:",e,t.changes)})},isAnonymous:function(){return!this.get("email")},isAdmin:function(){return this.get("is_admin")},loadFromApi:function(e,t){e=e||h.CURRENT_ID_STR,t=t||{};var i=this,n=t.success;return t.success=function(e,t){i.trigger("loaded",e,t),n&&n(e,t)},e===h.CURRENT_ID_STR&&(t.url=this.urlRoot+"/"+h.CURRENT_ID_STR),r.Model.prototype.fetch.call(this,t)},clearSessionStorage:function(){for(var e in sessionStorage)0===e.indexOf("history:")?sessionStorage.removeItem(e):"history-panel"===e&&sessionStorage.removeItem(e)},toString:function(){var e=[this.get("username")];return this.get("id")&&(e.unshift(this.get("id")),e.push(this.get("email"))),"User("+e.join(":")+")"}});h.CURRENT_ID_STR="current",h.getCurrentUserFromApi=function(e){var t=new h;return t.loadFromApi(h.CURRENT_ID_STR,e),t};r.Collection.extend(d.default.LoggableMixin).extend({model:h,urlRoot:function(){return Galaxy.root+"api/users"}});t.default={User:h}},function(e,t,i){"use strict";(function(e){function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}function a(e){return e&&e.__esModule?e:{default:e}}function s(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}function o(e,t){if(!e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return!t||"object"!=typeof t&&"function"!=typeof t?e:t}function r(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function, not "+typeof t);e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,enumerable:!1,writable:!0,configurable:!0}}),t&&(Object.setPrototypeOf?Object.setPrototypeOf(e,t):e.__proto__=t)}Object.defineProperty(t,"__esModule",{value:!0});var l=function(){function e(e,t){for(var i=0;i").addClass("bookmark").appendTo(s),r=e("").addClass("position").appendTo(o);e("").text(t).appendTo(r).click(function(){return a.view.go_to(t),!1});var l=e("").text(i).appendTo(o);if(n){var d=e("").addClass("delete-icon-container").prependTo(o).click(function(){return o.slideUp("fast"),o.remove(),a.view.has_changes=!0,!1});e("").addClass("icon-button delete").appendTo(d),l.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return this.view.has_changes=!0,o}},{key:"create_visualization",value:function(t,i,n,a,s){var o=this;return this.view=new m.default.TracksterView(h.extend(t,{header:!1})),this.view.editor=!0,e.when(this.view.load_chroms_deferred).then(function(e){var t=null;if(i){var r=i.chrom,l=i.start,d=i.end;t=i.overview,r&&void 0!==l&&d?o.view.change_chrom(r,l,d):o.view.change_chrom(e[0].chrom)}else o.view.change_chrom(e[0].chrom);if(n)for(var c=0;c"),e("#right-border").click(function(){t.ui.view.resize_window()}),window.force_right_panel("hide"),window.galaxy_config.app.id?this.view_existing():x.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()}},{key:"choose_existing_or_new",value:function(){var e=this,t=x.default.get("dbkey"),i={},n={dbkey:t,dataset_id:x.default.get("dataset_id"),hda_ldda:x.default.get("hda_ldda"),gene_region:x.default.get("gene_region")};t&&(i["f-dbkey"]=t),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"
You can add this dataset as:
a new track to one of your existing, saved Trackster sessions if they share the genome build: "+(t||"Not available.")+"
or create a new session with this dataset as the only track
",buttons:{Cancel:function(){window.top.location=Galaxy.root+"visualizations/list"},"View in saved visualization":function(){e.view_in_saved(n)},"View in new visualization":function(){e.view_new()}}})}},{key:"view_in_saved",value:function(t){var i=this,n=new C.default({url_base:Galaxy.root+"visualization/list_tracks",embedded:!0});Galaxy.modal.show({title:(0,c.default)("Add Data to Saved Visualization"),body:n.$el,buttons:{Cancel:function(){window.top.location=Galaxy.root+"visualizations/list"},"Add to visualization":function(){e(window.parent.document).find("input[name=id]:checked").each(function(){t.id=e(i).val(),window.top.location=Galaxy.root+"visualization/trackster?"+e.param(t)})}}})}},{key:"view_existing",value:function(){var t=window.galaxy_config.app.viz_config;this.ui.create_visualization({container:e("#center .unified-panel-body"),name:t.title,vis_id:t.vis_id,dbkey:t.dbkey},t.viewport,t.tracks,t.bookmarks,!0),this.init_editor()}},{key:"view_new",value:function(){var t=this;e.ajax({url:Galaxy.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(i){Galaxy.modal.show({title:(0,c.default)("New Visualization"),body:t.template_view_new(i),buttons:{Cancel:function(){window.top.location=Galaxy.root+"visualizations/list"},Create:function(){t.create_browser(e("#new-title").val(),e("#new-dbkey").val()),Galaxy.modal.hide()}}});var n=i.map(function(e){return e[1]});window.galaxy_config.app.default_dbkey&&h.contains(n,window.galaxy_config.app.default_dbkey)&&e("#new-dbkey").val(window.galaxy_config.app.default_dbkey),e("#new-title").focus(),e("select[name='dbkey']").select2(),e("#overlay").css("overflow","auto")}})}},{key:"template_view_new",value:function(e){for(var t=''}},{key:"init_editor",value:function(){var t=this;e("#center .unified-panel-title").text(this.ui.view.config.get_value("name")+" ("+this.ui.view.dbkey+")"),window.galaxy_config.app.add_dataset&&e.ajax({url:Galaxy.root+"api/datasets/"+window.galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){t.ui.view.add_drawable(m.default.object_from_template(e,t.ui.view,t.ui.view))}}),e("#add-bookmark-button").click(function(){var e=t.ui.view.chrom+":"+t.ui.view.low+"-"+t.ui.view.high;return t.ui.add_bookmark(e,"Bookmark description",!0)}),this.ui.init_keyboard_nav(this.ui.view),e(window).on("beforeunload",function(){if(t.ui.view.has_changes)return"There are unsaved changes to your visualization that will be lost if you leave this page."})}},{key:"create_browser",value:function(t,i){e(document).trigger("convert_to_values"),this.ui.create_visualization({container:e("#center .unified-panel-body"),name:t,dbkey:i},window.galaxy_config.app.gene_region),this.init_editor(),this.ui.view.editor=!0}}]),i}(p.View);t.default={TracksterUI:M,GalaxyApp:$}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}function a(e){return e&&e.__esModule?e:{default:e}}function s(e,t){j[e.attr("id")]=t}function o(t,i,n,a){n=".group",j[t.attr("id")]=a,t.bind("drag",{handle:"."+i,relative:!0},function(t,i){var a,s,o,r,l,d=e(this),c=d.parent(),u=c.children(".track,.group"),h=j[e(this).attr("id")];if(s=e(this).parents(n),0!==s.length){o=s.position().top,r=o+s.outerHeight();var f=j[s.attr("id")];if(i.offsetYr)return e(this).insertAfter(s),f.remove_drawable(h),void f.container.add_drawable(h)}for(s=null,l=0;l=o&&i.offsetY<=r)return i.offsetY-o0?l-1:l))}).bind("dragstart",function(){e(this).addClass("dragging")}).bind("dragend",function(){e(this).removeClass("dragging")})}function r(e,t){t||(t=0);var i=Math.pow(10,t);return Math.round(e*i)/i}function l(t){var i=e.Deferred();return e.ajax({type:"HEAD",url:t,beforeSend:function(e){e.setRequestHeader("Range","bytes=0-10")},success:function(e,t,n){i.resolve(206===n.status)}}),i}Object.defineProperty(t,"__esModule",{value:!0});var d=i(3),c=a(d),u=i(1),h=n(u),f=i(2),p=n(f),_=i(15),m=a(_),g=i(81),v=a(g),w=i(18),y=a(w),b=i(82),x=a(b),k=i(83),C=a(k),S=i(84),T=a(S),M=i(14),$=a(M),P=i(54),O=a(P),E=i(33),A=a(E),D=i(137),z=a(D);i(19);var I=h.extend,j={},L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G=["Histogram","Line","Filled","Intensity"],R=function e(t,i,n){if(e.id_counter||(e.id_counter=0),this.id=e.id_counter++,this.view=t,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=A.default.ConfigSettingCollection.from_models_and_saved_values(this.build_config_params(),n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new v.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var s=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){s.show()},function(){s.hide()})}};R.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(e){e.config.get_value("content_visible")?(e.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),e.hide_contents(),e.config.set_value("content_visible",!1)):(e.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),e.config.set_value("content_visible",!0),e.show_contents())}},{name:"settings_icon",title:(0,c.default)("Edit settings"),css_class:"gear",on_click_fn:function(e){new A.default.ConfigSettingCollectionView({collection:e.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:(0,c.default)("Remove"),css_class:"remove-icon",on_click_fn:function(t){e(".tooltip").remove(),t.remove()}}],I(R.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],build_config_params:function(){return this.config_params},config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(e){},to_dict:function(){},set_name:function(e){this.old_name=this.config.get_value("name"),this.config.set_value("name",e)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var t=this.view;this.container_div.hide(0,function(){e(this).remove(),t.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var N=function(e,t,i){R.call(this,e,t,i),this.obj_type=i.obj_type,this.drawables=[]};I(N.prototype,R.prototype,{unpack_drawables:function(e){this.drawables=[];for(var t,i=0;i").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),s(this.container_div,this),s(this.content_div,this),o(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new T.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(e("")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new T.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};I(V.prototype,R.prototype,N.prototype,{action_icons_def:[R.prototype.action_icons_def[0],R.prototype.action_icons_def[1],{name:"composite_icon",title:(0,c.default)("Show composite track"),css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_composite_track()}},{name:"filters_icon",title:(0,c.default)("Filters"),css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?(e.filters_manager.clear_filters(),e._restore_filter_managers()):(e.setup_multitrack_filtering(),e.request_draw({clear_tile_cache:!0})),e.filters_manager.toggle()}},R.prototype.action_icons_def[2]],build_container_div:function(){var t=e("").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(t),t},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var t=this.drawables.length;if(0===t)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===t)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof Z),this.action_icons.filters_icon.hide();else{var i,n,a,s=this.drawables[0].get_type(),o=0;for(i=0;i1&&o===this.drawables.length){var r,l={};for(a=this.drawables[0],n=0;n0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var e=0;e0){this.saved_filters_managers=[];for(var e=0;e").addClass("top-container").appendTo(t),this.browser_content_div=e("").addClass("content").appendTo(t),this.bottom_container=e("").addClass("bottom-container").appendTo(t),this.top_labeltrack=e("").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=e("").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,s(this.viewport_container,i),this.intro_div=e("").addClass("intro").appendTo(this.viewport_container),e("").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){m.default.select_datasets({dbkey:i.dbkey},function(e){h.each(e,function(e){i.add_drawable(re(e,i,i))})})}),this.nav_container=e("").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=e("").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=e("").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=e("").addClass("overview-viewport").appendTo(this.overview),this.overview_close=e("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=e("").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=e("").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=e("").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=e("").addClass("nav-controls").appendTo(this.nav),this.chrom_select=e("").attr({name:"chrom"}).addClass("chrom-nav").append("").appendTo(this.nav_controls);var n=function(t){"focusout"!==t.type&&13!==(t.keyCode||t.which)&&27!==(t.keyCode||t.which)||(27!==(t.keyCode||t.which)&&i.go_to(e(this).val()),e(this).hide(),e(this).val(""),i.location_span.show(),i.chrom_select.show()),t.stopPropagation()};this.nav_input=e("").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=e("").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(t,n){var a=[],s=e.map(i.get_tracks(ne),function(e){return e.data_manager.search_features(t.term).success(function(e){a=a.concat(e)})});e.when.apply(e,s).done(function(){n(e.map(a,function(e){return{label:e[0],value:e[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=e("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=e("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=e("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(t){e(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(e){i.zoom_in(e.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(e,t){this.current_x=t.offsetX}).bind("drag",function(e,t){var n=t.offsetX-this.current_x;this.current_x=t.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(e,t){if(e.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(e,t){t.original_low=i.low,t.current_height=e.clientY,t.current_x=t.offsetX}).bind("drag",function(t,n){var a=e(this),s=n.offsetX-n.current_x,o=a.scrollTop()-(t.clientY-n.current_height);a.scrollTop(o),n.current_height=t.clientY,n.current_x=n.offsetX;var r=Math.round(s/i.viewport_container.width()*(i.high-i.low));i.move_delta(r)}),this.top_labeltrack.bind("dragstart",function(t,n){return e("").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(e(this))}).bind("drag",function(t,n){e(n.proxy).css({left:Math.min(t.pageX,n.startX)-i.container.offset().left,width:Math.abs(t.pageX-n.startX)});var a=Math.min(t.pageX,n.startX)-i.container.offset().left,s=Math.max(t.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,r=i.viewport_container.width();i.update_location(Math.round(a/r*o)+i.low,Math.round(s/r*o)+i.low)}).bind("dragend",function(t,n){var a=Math.min(t.pageX,n.startX),s=Math.max(t.pageX,n.startX),o=i.high-i.low,r=i.viewport_container.width(),l=i.low;i.low=Math.round(a/r*o)+l,i.high=Math.round(s/r*o)+l,e(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new Q(this,{content_div:this.top_labeltrack})),e(window).bind("resize",function(){this.resize_timer&&window.clearTimeout(this.resize_timer),this.resize_timer=window.setTimeout(function(){i.resize_window()},500)}),e(document).bind("redraw",function(){i.redraw()}),this.reset(),e(window).trigger("resize")},get_base_color:function(e){return this.config.get_value(e.toLowerCase()+"_color")||this.config.get_value("n_color")}});I(H.prototype,N.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(e,t,i,n){var a=this;this.timer&&window.clearTimeout(this.timer),n?this.timer=window.setTimeout(function(){a.trigger("navigate",e+":"+t+"-"+i)},500):this.trigger("navigate",e+":"+t+"-"+i)},update_location:function(e,t){this.location_span.text(y.default.commatize(e)+" - "+y.default.commatize(t)),this.nav_input.val(this.chrom+":"+y.default.commatize(e)+"-"+y.default.commatize(t));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(t){var i=this;t.num=100;var n=e.Deferred();return e.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:t,dataType:"json",success:function(t){if(0!==t.chrom_info.length){if(t.reference){var a=new ee(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=t.chrom_info,i.chrom_select.html(""),i.chrom_select.append(e(''));for(var s=0,o=i.chrom_data.length;s");l.text(r),l.val(r),i.chrom_select.append(l)}t.prev_chroms&&i.chrom_select.append(e('')),t.next_chroms&&i.chrom_select.append(e('')),i.chrom_start_index=t.start_index,n.resolve(t.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+this.dbkey)}}),n},change_chrom:function(t,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(t,i,n)});if(t&&"None"!==t){if("previous"===t)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===t)return void a.load_chroms({low:this.chrom_start_index+100});var s=e.grep(a.chrom_data,function(e,i){return e.chrom===t})[0];if(void 0===s)return void a.load_chroms({chrom:t},function(){a.change_chrom(t,i,n)});if(t!==a.chrom){a.chrom=t,a.chrom_select.val(a.chrom),a.max_high=s.len-1,a.reset();for(var o=0,r=a.drawables.length;ot.max_high?(t.high=t.max_high,t.low=t.max_high-i):(t.high-=e,t.low-=e),t.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&window.clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=window.setTimeout(function(){t.request_redraw()},200);var n=t.chrom_select.val();this.trigger_navigate(n,t.low,t.high,!0)},add_drawable:function(e){N.prototype.add_drawable.call(this,e),e.init(),this.changed(),this.update_intro_div();var t=this;e.config.on("change",function(){t.changed()})},add_label_track:function(e){e.view=this,e.init(),this.label_tracks.push(e)},remove_drawable:function(t,i){if(N.prototype.remove_drawable.call(this,t),i){var n=this;t.container_div.hide(0,function(){e(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(e,t){var i=this,n=t?[t]:i.drawables;h.each(n,function(t){var n=h.find(i.tracks_to_be_redrawn,function(e){return e[0]===t});n?n[1]=e:i.tracks_to_be_redrawn.push([t,e])}),this.requested_redraw||(window.requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var e=this.low,t=this.high;ethis.max_high&&(t=this.max_high);var i=this.high-this.low;0!==this.high&&i").addClass("param-label").text(i.get("label")).appendTo(t),e("").addClass("param-input").html(i.get("html")).appendTo(t).find(":input").val(i.get("value")),e("").appendTo(t)},update_value:function(t){this.model.set_value(e(t.target).val())}}),q=p.View.extend({initialize:function(e){this.model.on("change:hidden",this.set_visible,this)},render:function(){var t=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).keydown(function(e){e.stopPropagation()}),e("
").addClass("param-row").appendTo(n),s=e("").attr("value","Run on complete dataset").appendTo(a);e("").attr("value","Run on visible region").appendTo(a).click(function(){t.run_on_region()}),s.click(function(){t.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var e=0;e").append(a),this.data=s,this.stale=!1};Y.prototype.predisplay_actions=function(){};var J=function(e,t,i,n,a){Y.call(this,e,t,i,n,a)};J.prototype.predisplay_actions=function(){};var W=function(e,t,i,n,a,s,o,r,l,d,c){Y.call(this,e,t,i,n,a),this.mode=s,this.all_slotted=r,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};I(W.prototype,Y.prototype),W.prototype.predisplay_actions=function(){};var X=function(t,i,n){I(n,{drag_handle_class:"draghandle"}),R.call(this,t,i,n),this.dataset=null,n.dataset&&(this.dataset=n.dataset instanceof p.Model?n.dataset:new $.default.Dataset(n.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in n?n.data_query_wait:5e3,this.data_manager="data_manager"in n?n.data_manager:new m.default.GenomeDataManager({dataset:this.dataset,genome:new m.default.Genome({key:t.dbkey,chroms_info:{chrom_info:t.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=e("
").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in n&&!n.resize||this.add_resize_handle())};I(X.prototype,R.prototype,{action_icons_def:[{name:"mode_icon",title:(0,c.default)("Set display mode"),css_class:"chevron-expand",on_click_fn:function(){}},R.prototype.action_icons_def[0],{name:"overview_icon",title:(0,c.default)("Set as overview"),css_class:"application-dock-270",on_click_fn:function(e){e.view.set_overview(e)}},R.prototype.action_icons_def[1],{name:"filters_icon",title:(0,c.default)("Filters"),css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?e.filters_manager.clear_filters():e.filters_manager.init_filters(),e.filters_manager.toggle()}},{name:"tools_icon",title:(0,c.default)("Tool"),css_class:"hammer",on_click_fn:function(t){t.tool.toggle(),t.tool.is_visible()?t.set_name(t.config.get_value("name")+t.tool_region_and_parameters_str()):t.revert_name(),e(".tooltip").remove()}},{name:"param_space_viz_icon",title:(0,c.default)("Tool parameter space visualization"),css_class:"arrow-split",on_click_fn:function(t){var i="\n Tool:"+t.tool.get("name")+" \n Dataset:"+t.config.get_value("name")+' \n Region(s):\n \n ',n=function(){Galaxy.modal.hide(),e(window).unbind("keypress.check_enter_esc")},a=function(){var i,n=e('select[name="regions"] option:selected').val(),a=new m.default.GenomeRegion({chrom:(void 0).view.chrom,start:(void 0).view.low,end:(void 0).view.high}),s=h.map(e(".bookmark"),function(t){return new m.default.GenomeRegion({from_str:e(t).children(".position").text()})});i="cur"===n?[a]:"bookmarks"===n?s:[a].concat(s),Galaxy.modal.hide(),window.top.location.href=Galaxy.root+"visualization/sweepster?"+e.param({dataset_id:t.dataset.id,hda_ldda:t.dataset.get("hda_ldda"),regions:JSON.stringify(new p.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:n,Yes:a}})}},R.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&R.prototype.can_draw.call(this)},build_container_div:function(){return e("").addClass("track").attr("id","track_"+this.id)},set_dataset:function(e){this.dataset=e,this.data_manager.set("dataset",e)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var t=this,i=!1,n=!1,a=e("
");e(t.container_div).hover(function(){t.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=e(t.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,t.min_height_px),t.max_height_px);e(t.tiles_div).css("height",a),t.visible_height_px=t.max_height_px===a?0:a,t.on_resize()}).bind("dragend",function(e,s){t.tile_cache.clear(),n=!1,i||a.hide(),t.config.set_value("height",t.visible_height_px),t.changed()}).appendTo(t.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof Q?"LabelTrack":this instanceof ee?"ReferenceTrack":this instanceof te?"LineTrack":this instanceof se?"ReadTrack":this instanceof ae?"VariantTrack":this instanceof Z?"CompositeTrack":this instanceof ne?"FeatureTrack":""},show_message:function(t){return this.tiles_div.remove(),e("").addClass("message").html(t).appendTo(this.content_div)},init:function(t){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=e("").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=e.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:t};return e.getJSON(this.dataset.url(),a,function(t){if(t&&"error"!==t&&"error"!==t.kind)"no converter"===t?(i.container_div.addClass("error"),i.show_message(L)):"no data"===t||void 0!==t.data&&(null===t.data||0===t.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===t?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),window.setTimeout(function(){i.init()},i.data_query_wait)):"data"!==t&&"data"!==t.status||(t.valid_chroms&&(i.valid_chroms=t.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,e.when.apply(e,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");t.message&&(a.append(e("").text("View error").click(function(){Galaxy.modal.show({title:(0,c.default)("Trackster Error"),body:"
"+t.message+"
",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(e("").text(" ")),a.append(e("").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_default_value("min_value",n),t.config.set_default_value("max_value",a),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var K=function(t,i,n){X.call(this,t,i,n);var a=this;if(o(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new T.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new F(h.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new m.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var s=new q({model:this.tool});s.render(),this.dynamic_tool_div=s.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=e("").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=e("").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};I(K.prototype,R.prototype,X.prototype,{action_icons_def:X.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(t){e(".tooltip").remove(),t.slotters[t.view.resolution_px_b].max_rows*=2,t.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(e){var t=this.to_dict();I(t,{data_manager:this.data_manager});var i=new this.constructor(this.view,e,t);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(e){this.filters_manager=e,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(isNaN(parseFloat(t.config.get_value("min_value")))||isNaN(parseFloat(t.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},change_mode:function(e){var t=this;return t.mode=e,t.config.set_value("mode",e),"Auto"===e&&this.data_manager.clear(),t.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+t.mode+")"),t},update_icons:function(){var e=this;e.action_icons.filters_icon.toggle(e.filters_available),e.action_icons.tools_icon.toggle(null!==e.tool),e.action_icons.param_space_viz_icon.toggle(null!==e.tool)},_gen_tile_cache_key:function(e,t){return e+"_"+t},request_draw:function(e){e&&e.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(e,this)},before_draw:function(){this.max_height_px=0},_draw:function(t){var i=this;if(this.can_draw()){var n=t&&t.clear_after,a=this.view.low,s=this.view.high,o=this.view.container.width(),r=this.view.resolution_px_b,l=1/r;this.is_overview&&(a=this.view.max_low,s=this.view.max_high,r=o/(this.view.max_high-this.view.max_low),l=1/r),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,c,u=Math.floor(400*l),f=Math.floor(a/u),p=[],_=[];f*u").text(d).make_text_editable({num_cols:12,on_finish:function(t){e(".tooltip").remove(),this.config.set_value(o,r(t,1)),i()},help_text:"Set "+s+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(e,t,i,n){var a=this;h.filter(e,function(e){return e instanceof J}).length>0?(this.max_height_px=0,h.each(e,function(e){e instanceof J||(e.html_elt.remove(),a.draw_helper(e.region,i,{force:!0,mode:"Coverage"}))}),this._add_yaxis_label("max")):(this.container_div.find(".yaxislabel").remove(),h.find(e,function(e){return e.has_icons})&&h.each(e,function(e){e.has_icons||e.html_elt.css("padding-top",20)}))},get_mode:function(e){return this.mode},update_auto_mode:function(e){},_get_drawables:function(){return[this]},draw_helper:function(t,i,n){var a=this;n||(n={});var s=n.force,o=n.mode||this.mode,r=1/i,l=this._get_drawables(),d=this._gen_tile_cache_key(i,t),c=s?void 0:this.tile_cache.get_elt(d);if(c)return function(e){return e&&"track"in e}(c)&&this.show_tile(c,i),c;if(!1===n.data_fetch)return null;var u=function(){var e=h.find(G,function(e){return e===o})?"Coverage":o,i=h.map(l,function(i){return i.data_manager.get_data(t,e,r,a.data_url_extra_params)});return a.view.reference_track&&i.push(a.view.reference_track.data_manager.get_data(t,o,r,a.view.reference_track.data_url_extra_params)),i},f=e.Deferred();return this.tile_cache.set_elt(d,f),e.when.apply(e,u()).then(function(){var s,o=u(),r=o;if(h.find(o,function(e){return y.default.is_deferred(e)}))return a.tile_cache.set_elt(d,void 0),void e.when(a.draw_helper(t,i,n)).then(function(e){f.resolve(e)});a.view.reference_track&&(s=a.view.reference_track.data_manager.subset_entry(o.pop(),t));var c=[],p=[];h.each(l,function(e,t){var n=r[t];"Auto"===e.mode&&(e.mode=e.get_mode(n),e.update_auto_mode(e.mode)),c.push(e.mode),p.push(e.get_canvas_height(n,e.mode,i,w))});var _,m=a.view.canvas_manager.new_canvas(),g=t.get("start"),v=t.get("end"),w=Math.ceil((v-g)*i)+a.left_offset,b=h.max(p);m.width=w,m.height=n.height||b;var x=m.getContext("2d");x.translate(a.left_offset,0),l.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),h.each(l,function(e,n){_=e.draw_tile(r[n],x,c[n],t,i,s)}),void 0!==_&&(a.tile_cache.set_elt(d,_),a.show_tile(_,i)),f.resolve(_)}),f},get_canvas_height:function(e,t,i,n){return this.visible_height_px},_draw_line_track_tile:function(e,t,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",h.max(h.map(e.data,function(e){return e[1]}))||0);var s=t.canvas;return new C.default.LinePainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new J(this,n,a,s,e.data)},draw_tile:function(e,t,i,n,a,s){},show_tile:function(e,t){var i=e.html_elt;e.predisplay_actions();var n=Math.round((e.low-(this.is_overview?this.view.max_low:this.view.low))*t);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(e){var t=this;return" - region=["+(void 0!==e?e.toString():"all")+"], parameters=["+h.values(t.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(e,t){return"Auto"===t||("Coverage"===t?"bigwig"===e.dataset_type:"bigwig"!==e.dataset_type&&"no_detail"!==e.extra_info)},can_subset:function(e){return!e.message&&"no_detail"!==e.extra_info&&("bigwig"!==e.dataset_type||e.data[1][0]-e.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var Q=function(e,t){X.call(this,e,t,{resize:!1,header:!1}),this.container_div.addClass("label-track")};I(Q.prototype,X.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(t){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),s=Math.floor(i.low/a)*a,o=this.view.container.width(),r=e("").addClass("label-container");s").addClass("pos-label").text(y.default.commatize(s)).css({left:l})),s+=a}this.content_div.children(":first").remove(),this.content_div.append(r)}});var Z=function(e,t,i){if(K.call(this,e,t,i),this.drawables=[],"drawables"in i){for(var n,a=0;athis.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}h.each(this.drawables,function(e){(e instanceof ne||e instanceof se)&&e.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};I(Z.prototype,K.prototype,{display_modes:G,build_config_params:function(){return h.union(R.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:(0,c.default)("Show individual tracks"),css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_group()}}].concat(K.prototype.action_icons_def),to_dict:N.prototype.to_dict,add_drawable:N.prototype.add_drawable,unpack_drawables:N.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var e=this.visible_height_px;h.each(this.drawables,function(t){t.visible_height_px=e}),X.prototype.on_resize.call(this)},change_mode:function(e){K.prototype.change_mode.call(this,e);for(var t=0;ts&&(s=o)}for(a=0;athis.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,s=K.prototype.draw_helper.call(this,e,t,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),s},can_subset:function(e){return!0},draw_tile:function(e,t,i,n,a){var s=this.data_manager.subset_entry(e,n),o=s.data,r=t.canvas;t.font=t.canvas.manager.default_font,t.textAlign="center";for(var l=0,d=o.length;l12e3?"Squish":"Pack"},get_canvas_height:function(e,t,i,n){if("Coverage"===t||"bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,e.data,t),s=new this.painter(null,null,null,this.config.to_key_value_dict(),t);return Math.max(this.min_height_px,s.get_required_height(a,n))},draw_tile:function(e,t,i,n,a,s,o){var r=this,l=t.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(e.data)for(var _=this.filters_manager.filters,m=0,g=e.data.length;m1){var r;if(0===this.container_div.find(".yaxislabel.variant").length&&(r=this.config.get_value("summary_height")/2,this.tiles_div.prepend(e("").text("Summary").addClass("yaxislabel variant top").css({"font-size":r+"px",top:(this.config.get_value("summary_height")-r)/2+"px"})),this.config.get_value("show_sample_data"))){var l=o.join(" ");this.tiles_div.prepend(e("").html(l).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}r=("Squish"===this.mode?5:10)+"px",e(this.tiles_div).find(".sample").css({"font-size":r,"line-height":r}),e(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var se=function(e,t,i){ne.call(this,e,t,i),this.painter=C.default.ReadPainter,this.update_icons()};I(se.prototype,R.prototype,K.prototype,ne.prototype,{build_config_params:function(){return h.union(R.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var oe={CompositeTrack:Z,DrawableGroup:V,DiagonalHeatmapTrack:ie,FeatureTrack:ne,LineTrack:te,ReadTrack:se,VariantTrack:ae,VcfTrack:ae},re=function(e,t,i){if("copy"in e)return e.copy(i);var n=e.obj_type;return n||(n=e.track_type),new oe[n](t,i,e)};t.default={TracksterView:H,DrawableGroup:V,LineTrack:te,FeatureTrack:ne,DiagonalHeatmapTrack:ie,ReadTrack:se,VariantTrack:ae,CompositeTrack:Z,object_from_template:re}}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(5),d=s(l),c=i(10),u=s(c),h=i(17),f=s(h),p=i(55),_=s(p),m=i(25),g=s(m),v=e.View.extend({initialize:function(e){var t=this;this.modal=parent.Galaxy.modal||new f.default.View,this.form=new _.default(d.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(e,i){var a=i.model.attributes,s="",o={},l=a.job_id;l?s=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(s=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),d.default.get({url:s,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),t._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),e.resolve()},error:function(t,s){var o=t&&t.err_msg||"Uncaught error.";401==s?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new u.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:(0,r.default)("Tool request failed"),body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",t),e.reject()}})},postchange:function(e,t){var i={tool_id:t.model.get("id"),tool_version:t.model.get("version"),inputs:n.extend(!0,{},t.data.create())};t.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),d.default.request({type:"POST",url:Galaxy.root+"api/tools/"+t.model.get("id")+"/build",data:i,success:function(i){t.update(i),t.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",t),e.reject()}})}},e)),this.deferred=this.form.deferred,this.setElement(""),this.$el.append(this.form.$el)},_customize:function(e){var t=this,i=e.model.attributes,n=new u.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:(0,r.default)("Execute"),cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),e.portlet.disable(),t.submit(i,function(){n.unwait(),e.portlet.enable()})}});if(i.buttons={execute:n},i.job_id&&i.job_remap){if("job_produced_collection_elements"===i.job_remap)var a="Replace elements in collection ?",s="The previous run of this tool failed. Use this option to replace the failed element(s) in the dataset collectio that were produced during the previous tool run.";else var a="Resume dependencies from this job ?",s="The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.";i.inputs.push({label:a,name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:s})}var o={};Galaxy.user.attributes.preferences&&"extra_user_preferences"in Galaxy.user.attributes.preferences&&(o=JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences)),"true"===("use_cached_job|use_cached_job_checkbox"in o&&o["use_cached_job|use_cached_job_checkbox"])&&i.inputs.push({label:"BETA: Attempt to re-use jobs with identical parameters ?",help:"This may skip executing jobs that you have already run",name:"use_cached_job",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["No",!1],["Yes",!0]]})},submit:function(e,t){var i=this,s={tool_id:e.id,tool_version:e.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(s))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(t&&t());if(e.action!==Galaxy.root+"tool_runner/index"){var o=n("").attr({action:e.action,method:e.method,enctype:e.enctype});return a.each(s.inputs,function(e,t){o.append(n("").attr({name:t,value:e}))}),o.hide().appendTo("body").submit().remove(),void(t&&t())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",s),d.default.request({type:"POST",url:Galaxy.root+"api/tools",data:s,success:function(e){if(t&&t(),i.$el.children().hide(),i.$el.append(i._templateSuccess(e)),e.jobs&&e.jobs.length>0){i.$el.append(n("",{id:"webhook-view"}));new g.default.WebhookView({type:"tool",toolId:s.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){t&&t(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var n=!1;if(e&&e.err_data){var a=i.form.data.matchResponse(e.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:(0,r.default)("Job submission failed"),body:i._templateError(s,e&&e.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(e){var t=this,i=e.inputs,n=-1,a=null;for(var s in i){var o=i[s],r=this.form.data.match(s),l=this.form.field_list[r],d=this.form.input_list[r];if(r&&d&&l){if(!d.optional&&null==o)return this.form.highlight(r),!1;if(l.validate){var c=function(){t.form.trigger("reset")},u=l.validate(c);if(!u.valid)return this.form.highlight(r,u.message),!1}if(o&&o.batch){var h=o.values.length,f=h>0&&o.values[0]&&o.values[0].src;if(f)if(null===a)a=f;else if(a!==f)return this.form.highlight(r,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===n)n=h;else if(n!==h)return this.form.highlight(r,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+h+" selection(s) while a previous field contains "+n+"."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",s=n("").addClass("donemessagelarge").append(n("").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(e.outputs,function(e){s.append(n("").addClass("messagerow").append(n("").text(e.hid+": "+e.name)))}),s.append(n("").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),s}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return n("").addClass("errormessagelarge").append(n("").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. 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",(0,p.default)(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"
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",(0,v.default)(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"
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",(0,v.default)(['Unpaired datasets are shown in the unpaired section ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the paired section.',"
To pair datasets, you can:","
Click a dataset in the ",'forward column ',"to select it then click a dataset in the ",'reverse column.',"
",'
Click one of the "Pair these datasets" buttons in the ','middle column ',"to pair the datasets in a particular row.","
",'
Click "Auto-pair" ',"to have your datasets automatically paired based on name.","
","
"].join("")),"","
",(0,v.default)(["
You can filter what is shown in the unpaired sections by:","
Entering partial dataset names in either the ",'forward filter or ','reverse filter.',"
","
Choosing from a list of preset filters by clicking the ",'"Choose filters" link.',"
Clearing the filters by clicking the ",'"Clear filters" link.',"
","
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\n \n \x3c!--\n \n --\x3e\n \n
\n '}})}).call(t,i(2),i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(10),s=n(a),o=i(655),r=n(o),l=i(656),d=n(l),c=i(3),u=n(c),h=e.View.extend({initialize:function(t,i){var n=this;this.userIsAnonymous=Galaxy.user.isAnonymous(),this.allow_user_dataset_purge=i.config.allow_user_dataset_purge,this.root=i.root,this.historyView=new d.default.CurrentHistoryView({className:d.default.CurrentHistoryView.prototype.className+" middle",purgeAllowed:this.allow_user_dataset_purge,linkTarget:"galaxy_main"}),Galaxy.currHistoryPanel=this.historyView,Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),this.buttonRefresh=new s.default.ButtonLink({id:"history-refresh-button",title:(0,u.default)("Refresh history"),cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){n.historyView.loadCurrentHistory()}}),this.buttonOptions=new s.default.ButtonLink({id:"history-options-button",title:(0,u.default)("History options"),cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:this.root+"root/history_options"}),this.buttonViewMulti=new s.default.ButtonLink({id:"history-view-multi-button",title:(0,u.default)("View all histories"),cls:"panel-header-button",icon:"fa fa-columns",href:this.root+"history/view_multiple"}),this.model=new e.Model({cls:"history-right-panel",title:(0,u.default)("History"),buttons:[this.buttonRefresh,this.buttonOptions,this.buttonViewMulti]}),this.setElement(this._template()),this.historyView.setElement(this.$el),this.historyView.connectToQuotaMeter(Galaxy.quotaMeter),this.historyView.loadCurrentHistory(),Galaxy.listenTo(this.historyView,"history-size-change",function(){Galaxy.user.fetch({url:Galaxy.user.urlRoot()+"/"+(Galaxy.user.id||"current")})})},render:function(){this.optionsMenu=(0,r.default)(this.buttonOptions.$el,{anonymous:this.userIsAnonymous,purgeAllowed:this.allow_user_dataset_purge,root:this.root}),this.buttonViewMulti.$el[this.userIsAnonymous?"hide":"show"]()},_template:function(e){return[''].join("")},toString:function(){return"historyPanel"}});t.default=h}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function a(e,t,i){return o.clone(_).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target=n.target||"galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}Object.defineProperty(t,"__esModule",{value:!0});var s=i(1),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=i(3),l=n(r),d=i(41),c=n(d),u=i(143),h=n(u),f=i(25),p=n(f),_=[{html:(0,l.default)("History Lists"),header:!0},{html:(0,l.default)("Saved Histories"),href:"histories/list",target:"_top"},{html:(0,l.default)("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:(0,l.default)("Current History"),header:!0,anon:!0},{html:(0,l.default)("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:(0,l.default)("Copy History"),func:function(){(0,h.default)(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Share or Publish"),href:"history/sharing"},{html:(0,l.default)("Show Structure"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/show_structure")}},{html:(0,l.default)("Extract Workflow"),href:"workflow/build_from_current_history"},{html:(0,l.default)("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete the current history?"))&&Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete the current history permanently? This cannot be undone."))&&Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Dataset Actions"),header:!0,anon:!0},{html:(0,l.default)("Copy Datasets"),href:"dataset/copy_datasets"},{html:(0,l.default)("Dataset Security"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/permissions?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,l.default)("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:(0,l.default)("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:(0,l.default)("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really unhide all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Purge Deleted Datasets"),confirm:(0,l.default)("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:(0,l.default)("Downloads"),header:!0},{html:(0,l.default)("Export Tool Citations"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/citations?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,l.default)("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:(0,l.default)("Other Actions"),header:!0},{html:(0,l.default)("Import from File"),href:"histories/import",target:"_top"}];p.default.load({type:"history-menu",async:!1,callback:function(t){var i=[];t.each(function(e){var t=e.toJSON();t.activate&&i.push({html:(0,l.default)(t.config.title),anon:!0})}),i.length>0&&(i.unshift({html:(0,l.default)("Webhooks"),header:!0}),e.merge(_,i))}});var m=function(e,t){t=t||{};var i=void 0===t.anonymous||t.anonymous,n=t.purgeAllowed||!1,s=a(i,n,Galaxy.root);return new c.default(e,s)};t.default=m}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(144),r=(s(o),i(176)),l=s(r),d=i(6),c=s(d),u=i(3),h=s(u),f=c.default.SessionStorageModel.extend({defaults:{tagsEditorShown:!1,annotationEditorShown:!1,scrollPosition:0},toString:function(){return"HistoryViewPrefs("+JSON.stringify(this.toJSON())+")"}});f.storageKey=function(){return"history-panel"};var p=l.default.HistoryViewEdit,_=p.extend({className:p.prototype.className+" current-history-panel",HDCAViewClass:p.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),emptyMsg:[(0,h.default)("This history is empty"),". ",(0,h.default)("You can "),'',(0,h.default)("load your own data"),"",(0,h.default)(" or "),'',(0,h.default)("get data from an external source"),""].join(""),initialize:function(t){t=t||{},this.preferences=new f(e.extend({id:f.storageKey()},e.pick(t,e.keys(f.prototype.defaults)))),p.prototype.initialize.call(this,t),this.panelStack=[],this.currentContentId=t.currentContentId||null},_setUpListeners:function(){p.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",(0,h.default)("You must be logged in to switch histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(e,{url:Galaxy.root+"history/set_as_current?id="+e})},createNewHistory:function(e){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to create histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(null,{url:Galaxy.root+"history/create_new_current"})},setModel:function(e,t,i){return p.prototype.setModel.call(this,e,t,i),this.model&&this.model.id&&(this.log("checking for updates"),this.model.checkForUpdates()),this},_setUpModelListeners:function(){return p.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(){p.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(t){t=t||this.$el;var i=this;return p.prototype._setUpBehaviors.call(i,t),this._debouncedScrollCaptureHandler||(this._debouncedScrollCaptureHandler=e.debounce(function(){i.$el.is(":visible")&&i.preferences.set("scrollPosition",n(this).scrollTop())},40)),i.$scrollContainer(t).off("scroll",this._debouncedScrollCaptureHandler).on("scroll",this._debouncedScrollCaptureHandler),i},_buildNewRender:function(){if(!this.model)return n();var e=p.prototype._buildNewRender.call(this);return e.find(".search").prependTo(e.find("> .controls")),this._renderQuotaMessage(e),e},_renderQuotaMessage:function(e){return e=e||this.$el,n(this.templates.quotaMsg({},this)).prependTo(e.find(".messages"))},_renderTags:function(e){var t=this;p.prototype._renderTags.call(t,e),t.preferences.get("tagsEditorShown")&&t.tagsEditor.toggle(!0),t.listenTo(t.tagsEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("tagsEditorShown",e.hidden)})},_renderAnnotation:function(e){var t=this;p.prototype._renderAnnotation.call(t,e),t.preferences.get("annotationEditorShown")&&t.annotationEditor.toggle(!0),t.listenTo(t.annotationEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("annotationEditorShown",e.hidden)})},_swapNewRender:function(t){p.prototype._swapNewRender.call(this,t);var i=this;return e.delay(function(){var e=i.preferences.get("scrollPosition");e&&i.scrollTo(e,0)},10),this},_attachItems:function(e){p.prototype._attachItems.call(this,e);var t=this;return t.currentContentId&&t._setCurrentContentById(t.currentContentId),this},addItemView:function(e,t,i){var n=p.prototype.addItemView.call(this,e,t,i);return n&&this.panelStack.length?this._collapseDrilldownPanel():n},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}})},setCurrentContent:function(e){this.$(".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.$list()).show()},events:e.extend(e.clone(p.prototype.events),{"click .uploader-link":function(e){Galaxy.upload.show(e)},"click .get-data-link":function(e){var t=n(".toolMenuContainer");t.parent().scrollTop(0),t.find('span:contains("Get Data")').click()}}),listenToGalaxy:function(t){this.listenTo(t,{"center-frame:load":function(t){var i=t.fullpath,n=null,a={display:/datasets\/([a-f0-9]+)\/display/,edit:/datasets\/([a-f0-9]+)\/edit/,report_error:/dataset\/errors\?id=([a-f0-9]+)/,rerun:/tool_runner\/rerun\?id=([a-f0-9]+)/,show_params:/datasets\/([a-f0-9]+)\/show_params/};e.find(a,function(t,a){return n=e.result(i.match(t),1)}),this._setCurrentContentById(n?"dataset-"+n:null)},"center-panel:load":function(e){this._setCurrentContentById()}})},connectToQuotaMeter:function(e){return e?(this.listenTo(e,"quota:over",this.showQuotaMessage),this.listenTo(e,"quota:under",this.hideQuotaMessage),this.on("rendered rendered:initial",function(){e&&e.isOverQuota()&&this.showQuotaMessage()}),this):this},clearMessages:function(t){var i=e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget);return i=i.not(".quota-message"),i.fadeOut(this.fxSpeed,function(){n(this).remove()}),this},showQuotaMessage:function(){var e=this.$(".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((0,h.default)("Really unhide all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{visible:!0}).done(function(){e.model.contents.includeHidden||e.renderItems()}):a.when()},deleteHidden:function(){var e=this;return confirm((0,h.default)("Really delete all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{deleted:!0,visible:!0}):a.when()},toString:function(){return"CurrentHistoryView("+(this.model?this.model.get("name"):"")+")"}});_.prototype.templates=function(){var t=c.default.wrapTemplate(['
',(0,h.default)("You are over your disk quota"),". ",(0,h.default)("Tool execution is on hold until your disk usage drops below your allocated quota"),".","
"],"history");return e.extend(e.clone(p.prototype.templates),{quotaMsg:t})}(),t.default={CurrentHistoryView:_}}).call(t,i(1),i(0),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(26),d=(s(l),i(10)),c=s(d),u=i(32),h=s(u),f=e.Model.extend({initialize:function(e){e=e||{},e.user_id=e.user_id||Galaxy.user.id,this.set({user_id:e.user_id,information:{title:(0,r.default)("Manage information"),description:"Edit your email, addresses and custom parameters or change your username.",url:"api/users/"+e.user_id+"/information/inputs",icon:"fa-user",redirect:"user"},password:{title:(0,r.default)("Change password"),description:(0,r.default)("Allows you to change your login credentials."),icon:"fa-unlock-alt",url:"api/users/"+e.user_id+"/password/inputs",submit_title:"Save password",redirect:"user"},communication:{title:(0,r.default)("Change communication settings"),description:(0,r.default)("Enable or disable the communication feature to chat with other users."),url:"api/users/"+e.user_id+"/communication/inputs",icon:"fa-comments-o",redirect:"user"},permissions:{title:(0,r.default)("Set dataset permissions for new histories"),description:"Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.",url:"api/users/"+e.user_id+"/permissions/inputs",icon:"fa-users",submit_title:"Save permissions",redirect:"user"},api_key:{title:(0,r.default)("Manage API key"),description:(0,r.default)("Access your current API key or create a new one."),url:"api/users/"+e.user_id+"/api_key/inputs",icon:"fa-key",submit_title:"Create a new key",submit_icon:"fa-check"},toolbox_filters:{title:(0,r.default)("Manage Toolbox filters"),description:(0,r.default)("Customize your Toolbox by displaying or omitting sets of Tools."),url:"api/users/"+e.user_id+"/toolbox_filters/inputs",icon:"fa-filter",submit_title:"Save filters",redirect:"user"},openids:{title:(0,r.default)("Manage OpenIDs"),description:(0,r.default)("Associate OpenIDs with your account."),icon:"fa-openid",onclick:function(){window.location.href=Galaxy.root+"openids/list"}},custom_builds:{title:(0,r.default)("Manage custom builds"),description:(0,r.default)("Add or remove custom builds using history datasets."),icon:"fa-cubes",onclick:function(){window.location.href=Galaxy.root+"custom_builds"}},logout:{title:(0,r.default)("Sign out"),description:(0,r.default)("Click here to sign out of all sessions."),icon:"fa-sign-out",onclick:function(){Galaxy.modal.show({title:(0,r.default)("Sign out"),body:"Do you want to continue and sign out of all active sessions?",buttons:{Cancel:function(){Galaxy.modal.hide()},"Sign out":function(){window.location.href=Galaxy.root+"user/logout?session_csrf_token="+Galaxy.session_csrf_token}}})}}})}}),p=e.View.extend({title:(0,r.default)("User Preferences"),active_tab:"user",initialize:function(){this.model=new f,this.setElement(""),this.render()},render:function(){var e=this,t=Galaxy.config;n.getJSON(Galaxy.root+"api/users/"+Galaxy.user.id,function(i){e.$preferences=n("").addClass("ui-panel").append(n("").append("User preferences")).append(n("").append("You are logged in as "+a.escape(i.email)+".")).append(e.$table=n("
You are using '+e.nice_total_disk_usage+" of disk space in this Galaxy instance. "+(Galaxy.config.enable_quotas?"Your disk quota is: "+e.quota+". ":"")+'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.
'}});t.default={View:p,Model:f}}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=a(s),r=i(5),l=(a(r),i(10)),d=a(l),c=i(26),u=a(c),h=i(659),f=a(h),p=e.Collection.extend({comparator:function(e,t){return e=e.get("name"),t=t.get("name"),e>t?1:e").append(n("").text("Current Custom Builds")).append(this.table.$el).append(this.$installed=n("").append(n("").text("System Installed Builds").addClass("ui-margin-top")).append(this.installed_builds.$el)).append(n("").text("Add a Custom Build").addClass("ui-margin-top")).append(n("").addClass("ui-column").append(n("").addClass("ui-column-left").append(this.message.$el).append(this.$form=n("").addClass("ui-margin-top"))).append(this.$help=n("").addClass("ui-column-right")))),this.listenTo(this.collection,"add remove reset",function(){i._renderTable()}),this.listenTo(this.model,"change",function(){i._renderForm()}),this.collection.fetch(),this.model.fetch()},render:function(){this._renderTable(),this._renderForm()},_renderTable:function(){var e=this;this.table.delAll(),this.collection.sort(),this.collection.each(function(t){e.table.add(t.get("name")),e.table.add(t.id),e.table.add(void 0!==t.get("count")?t.get("count"):"Processing..."),e.table.add(new d.default.ButtonIcon({icon:"fa-trash-o",cls:"ui-button-icon-plain",tooltip:(0,o.default)("Delete custom build."),onclick:function(){t.destroy()}}).$el),e.table.append(t.id)})},_renderForm:function(){var e=this,t=new u.default({inputs:[{type:"text",name:"name",label:"Name",help:"Specify a build name e.g. Hamster."},{type:"text",name:"id",label:"Key",help:"Specify a build key e.g. hamster_v1."},{name:"len",type:"conditional",test_param:{name:"type",label:"Definition",help:(0,o.default)("Provide the data source."),type:"select",value:"fasta",data:[{value:"fasta",label:"FASTA-file from history"},{value:"file",label:"Len-file from disk"},{value:"text",label:"Len-file by copy/paste"}]},cases:[{value:"fasta",inputs:[{type:"select",name:"value",label:"FASTA-file",data:this.model.get("fasta_hdas")}]},{value:"file",inputs:[{type:"upload",name:"value",label:"Len-file",data:this.model.get("len_hdas")}]},{value:"text",inputs:[{type:"text",area:!0,name:"value",label:"Edit/Paste"}]}]}],buttons:{save:new d.default.Button({icon:"fa-save",tooltip:(0,o.default)("Create new Build"),title:(0,o.default)("Save"),cls:"btn btn-primary ui-clear-float",onclick:function(){var i=t.data.create();i.id&&i.name?e.collection.create(i,{wait:!0,success:function(t){t.get("message")?e.message.update({message:t.get("message"),status:"warning"}):e.message.update({message:"Successfully added a new custom build.",status:"success"})},error:function(t,i){var n=i&&i.responseJSON&&i.responseJSON.err_msg;e.message.update({message:n||"Failed to create custom build.",status:"danger"})}}):e.message.update({message:"All inputs are required.",status:"danger"})}})},onchange:function(){var i=t.data.match("len|type");if(i){var n=t.field_list[i];e._renderHelp(n.value())}}});this.$form.empty().append(t.$el);var i=this.model.get("installed_builds");i&&i.length?(this.$installed.show(),this.installed_builds.update(this.model.get("installed_builds"))):this.$installed.hide(),this._renderHelp("fasta")},_renderHelp:function(e){this.$help.empty().addClass("alert alert-info").html("fasta"==e?this._templateFasta():this._templateLen())},_templateLen:function(){return"
Length Format
The length format is two-column, separated by whitespace, of the form:
chrom/contig length of chrom/contig
For example, the first few entries of mm9.len are as follows:
Trackster uses this information to populate the select box for chrom/contig, andto set the maximum basepair of the track browser. You may either upload a .len fileof this format (Len File option), or directly enter the information into the box (Len Entry option).
"},_templateFasta:function(){return"
FASTA format
This is a multi-fasta file from your current history that provides the genomesequences for each chromosome/contig in your build.
Here is a snippet from an example multi-fasta file:
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'}}),x=l.View.extend({title:(0,v.default)("Workflows"),active_tab:"workflow",initialize:function(){y.default.markViewAsLoading(this),c.bindAll(this,"adjustActiondropdown"),this.collection=new p.default.WorkflowCollection,this.collection.fetch().done(this.render()),this.collection.bind("add",this.appendItem),this.collection.on("sync",this.render,this)},events:{dragleave:"unhighlightDropZone",drop:"drop",dragover:function(t){e(".hidden_description_layer").addClass("dragover"),e(".menubutton").addClass("background-none"),t.preventDefault()}},unhighlightDropZone:function(){e(".hidden_description_layer").removeClass("dragover"),e(".menubutton").removeClass("background-none")},drop:function(e){this.unhighlightDropZone(),e.preventDefault();for(var t,i=e.dataTransfer.files,n=0;t=i[n];n++)this.readWorkflowFiles(t)},readWorkflowFiles:function(e){var t=this,i=new FileReader;i.onload=function(n){var a=void 0;try{a=JSON.parse(i.result)}catch(t){o.error("Could not read file '"+e.name+"'. Verify it is a valid Galaxy workflow"),a=null}a&&t.collection.create(a,{at:0,wait:!0,success:function(){o.success("Successfully imported workflow '"+a.name+"'")},error:function(e,t,i){o.error(i.errorThrown)}})},i.readAsText(e,"utf-8")},_showArgErrors:c.once(function(){var e=m.default.get("message");"error"===m.default.get("status")?o.error(c.escape(e||"Unknown Error, please report this to an administrator.")):e&&o.info(c.escape(e))}),render:function(){var e=this,t=this._templateHeader(),i=this._templateActionButtons(),n=this._templateWorkflowTable();this.$el.html(t+i+n),c.each(this.collection.models,function(t){e.appendItem(t),e.confirmDelete(t)});return this.searchWorkflow(this.$(".search-wf"),this.$(".workflow-search tr"),3),this.adjustActiondropdown(),this._showArgErrors(),this},appendItem:function(t){var i=new b({model:t,collection:this.collection});e(".workflow-search").append(i.render().el),i.renderTagEditor()},confirmDelete:function(e){this.$(".link-confirm-shared-"+e.id).click(function(){return window.confirm("Are you sure you want to remove the shared workflow '"+e.attributes.name+"'?")})},searchWorkflow:function(t,i,n){t.on("keyup",function(){var t=e(this).val();if(t.length>=n){var a=new RegExp(t,"i");i.hide(),i.filter(function(){return a.test(e(this).text())}).show()}else i.show()})},adjustActiondropdown:function(){e(this.el).on("show.bs.dropdown",function(){e(this.el).css("overflow","inherit")}),e(this.el).on("hide.bs.dropdown",function(){e(this.el).css("overflow","auto")})},_templateNoWorkflow:function(){return'
You have no workflows.
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Name
Tags
Owner
# of Steps
Published
Show in tools panel
Drop workflow files here to import
'},_templateHeader:function(){return'
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Dataset Error
\n
An error occured while running the tool "+t.tool_id+'.
\n
Tool execution generated the following messages:
\n
'+n.escape(t.stderr)+"
\n
Report This Error
\n
\n Usually the local Galaxy administrators regularly review errors that occur on the server\n However, if you would like to provide additional information (such as what you were trying\n to do when the error occurred) and a contact e-mail address, we will be better able to\n investigate your problem and get back to you.\n
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i,n,a,s=this.drawables[0].get_type(),o=0;for(i=0;i1&&o===this.drawables.length){var r,l={};for(a=this.drawables[0],n=0;n0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var e=0;e0){this.saved_filters_managers=[];for(var e=0;e").addClass("top-container").appendTo(t),this.browser_content_div=e("").addClass("content").appendTo(t),this.bottom_container=e("").addClass("bottom-container").appendTo(t),this.top_labeltrack=e("").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=e("").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,s(this.viewport_container,i),this.intro_div=e("").addClass("intro").appendTo(this.viewport_container),e("").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){m.default.select_datasets({dbkey:i.dbkey},function(e){h.each(e,function(e){i.add_drawable(re(e,i,i))})})}),this.nav_container=e("").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=e("").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=e("").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=e("").addClass("overview-viewport").appendTo(this.overview),this.overview_close=e("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=e("").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=e("").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=e("").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=e("").addClass("nav-controls").appendTo(this.nav),this.chrom_select=e("").attr({name:"chrom"}).addClass("chrom-nav").append("").appendTo(this.nav_controls);var n=function(t){"focusout"!==t.type&&13!==(t.keyCode||t.which)&&27!==(t.keyCode||t.which)||(27!==(t.keyCode||t.which)&&i.go_to(e(this).val()),e(this).hide(),e(this).val(""),i.location_span.show(),i.chrom_select.show()),t.stopPropagation()};this.nav_input=e("").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=e("").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(t,n){var a=[],s=e.map(i.get_tracks(ne),function(e){return e.data_manager.search_features(t.term).success(function(e){a=a.concat(e)})});e.when.apply(e,s).done(function(){n(e.map(a,function(e){return{label:e[0],value:e[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=e("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=e("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=e("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(t){e(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(e){i.zoom_in(e.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(e,t){this.current_x=t.offsetX}).bind("drag",function(e,t){var n=t.offsetX-this.current_x;this.current_x=t.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(e,t){if(e.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(e,t){t.original_low=i.low,t.current_height=e.clientY,t.current_x=t.offsetX}).bind("drag",function(t,n){var a=e(this),s=n.offsetX-n.current_x,o=a.scrollTop()-(t.clientY-n.current_height);a.scrollTop(o),n.current_height=t.clientY,n.current_x=n.offsetX;var r=Math.round(s/i.viewport_container.width()*(i.high-i.low));i.move_delta(r)}),this.top_labeltrack.bind("dragstart",function(t,n){return e("").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(e(this))}).bind("drag",function(t,n){e(n.proxy).css({left:Math.min(t.pageX,n.startX)-i.container.offset().left,width:Math.abs(t.pageX-n.startX)});var a=Math.min(t.pageX,n.startX)-i.container.offset().left,s=Math.max(t.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,r=i.viewport_container.width();i.update_location(Math.round(a/r*o)+i.low,Math.round(s/r*o)+i.low)}).bind("dragend",function(t,n){var a=Math.min(t.pageX,n.startX),s=Math.max(t.pageX,n.startX),o=i.high-i.low,r=i.viewport_container.width(),l=i.low;i.low=Math.round(a/r*o)+l,i.high=Math.round(s/r*o)+l,e(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new Q(this,{content_div:this.top_labeltrack})),e(window).bind("resize",function(){this.resize_timer&&window.clearTimeout(this.resize_timer),this.resize_timer=window.setTimeout(function(){i.resize_window()},500)}),e(document).bind("redraw",function(){i.redraw()}),this.reset(),e(window).trigger("resize")},get_base_color:function(e){return this.config.get_value(e.toLowerCase()+"_color")||this.config.get_value("n_color")}});I(H.prototype,N.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(e,t,i,n){var a=this;this.timer&&window.clearTimeout(this.timer),n?this.timer=window.setTimeout(function(){a.trigger("navigate",e+":"+t+"-"+i)},500):this.trigger("navigate",e+":"+t+"-"+i)},update_location:function(e,t){this.location_span.text(y.default.commatize(e)+" - "+y.default.commatize(t)),this.nav_input.val(this.chrom+":"+y.default.commatize(e)+"-"+y.default.commatize(t));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(t){var i=this;t.num=100;var n=e.Deferred();return e.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:t,dataType:"json",success:function(t){if(0!==t.chrom_info.length){if(t.reference){var a=new ee(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=t.chrom_info,i.chrom_select.html(""),i.chrom_select.append(e(''));for(var s=0,o=i.chrom_data.length;s");l.text(r),l.val(r),i.chrom_select.append(l)}t.prev_chroms&&i.chrom_select.append(e('')),t.next_chroms&&i.chrom_select.append(e('')),i.chrom_start_index=t.start_index,n.resolve(t.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+this.dbkey)}}),n},change_chrom:function(t,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(t,i,n)});if(t&&"None"!==t){if("previous"===t)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===t)return void a.load_chroms({low:this.chrom_start_index+100});var s=e.grep(a.chrom_data,function(e,i){return e.chrom===t})[0];if(void 0===s)return void a.load_chroms({chrom:t},function(){a.change_chrom(t,i,n)});if(t!==a.chrom){a.chrom=t,a.chrom_select.val(a.chrom),a.max_high=s.len-1,a.reset();for(var o=0,r=a.drawables.length;ot.max_high?(t.high=t.max_high,t.low=t.max_high-i):(t.high-=e,t.low-=e),t.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&window.clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=window.setTimeout(function(){t.request_redraw()},200);var n=t.chrom_select.val();this.trigger_navigate(n,t.low,t.high,!0)},add_drawable:function(e){N.prototype.add_drawable.call(this,e),e.init(),this.changed(),this.update_intro_div();var t=this;e.config.on("change",function(){t.changed()})},add_label_track:function(e){e.view=this,e.init(),this.label_tracks.push(e)},remove_drawable:function(t,i){if(N.prototype.remove_drawable.call(this,t),i){var n=this;t.container_div.hide(0,function(){e(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(e,t){var i=this,n=t?[t]:i.drawables;h.each(n,function(t){var n=h.find(i.tracks_to_be_redrawn,function(e){return e[0]===t});n?n[1]=e:i.tracks_to_be_redrawn.push([t,e])}),this.requested_redraw||(window.requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var e=this.low,t=this.high;ethis.max_high&&(t=this.max_high);var i=this.high-this.low;0!==this.high&&i").addClass("param-label").text(i.get("label")).appendTo(t),e("").addClass("param-input").html(i.get("html")).appendTo(t).find(":input").val(i.get("value")),e("").appendTo(t)},update_value:function(t){this.model.set_value(e(t.target).val())}}),q=p.View.extend({initialize:function(e){this.model.on("change:hidden",this.set_visible,this)},render:function(){var t=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).keydown(function(e){e.stopPropagation()}),e("
").addClass("param-row").appendTo(n),s=e("").attr("value","Run on complete dataset").appendTo(a);e("").attr("value","Run on visible region").appendTo(a).click(function(){t.run_on_region()}),s.click(function(){t.run_on_dataset()}),i.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var e=0;e").append(a),this.data=s,this.stale=!1};Y.prototype.predisplay_actions=function(){};var J=function(e,t,i,n,a){Y.call(this,e,t,i,n,a)};J.prototype.predisplay_actions=function(){};var W=function(e,t,i,n,a,s,o,r,l,d,c){Y.call(this,e,t,i,n,a),this.mode=s,this.all_slotted=r,this.feature_mapper=l,this.has_icons=!1,this.incomplete_features=d,this.other_tiles_features_drawn={},this.seq_data=c};I(W.prototype,Y.prototype),W.prototype.predisplay_actions=function(){};var X=function(t,i,n){I(n,{drag_handle_class:"draghandle"}),R.call(this,t,i,n),this.dataset=null,n.dataset&&(this.dataset=n.dataset instanceof p.Model?n.dataset:new $.default.Dataset(n.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in n?n.data_query_wait:5e3,this.data_manager="data_manager"in n?n.data_manager:new m.default.GenomeDataManager({dataset:this.dataset,genome:new m.default.Genome({key:t.dbkey,chroms_info:{chrom_info:t.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=e("
").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in n&&!n.resize||this.add_resize_handle())};I(X.prototype,R.prototype,{action_icons_def:[{name:"mode_icon",title:(0,c.default)("Set display mode"),css_class:"chevron-expand",on_click_fn:function(){}},R.prototype.action_icons_def[0],{name:"overview_icon",title:(0,c.default)("Set as overview"),css_class:"application-dock-270",on_click_fn:function(e){e.view.set_overview(e)}},R.prototype.action_icons_def[1],{name:"filters_icon",title:(0,c.default)("Filters"),css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?e.filters_manager.clear_filters():e.filters_manager.init_filters(),e.filters_manager.toggle()}},{name:"tools_icon",title:(0,c.default)("Tool"),css_class:"hammer",on_click_fn:function(t){t.tool.toggle(),t.tool.is_visible()?t.set_name(t.config.get_value("name")+t.tool_region_and_parameters_str()):t.revert_name(),e(".tooltip").remove()}},{name:"param_space_viz_icon",title:(0,c.default)("Tool parameter space visualization"),css_class:"arrow-split",on_click_fn:function(t){var i="\n Tool:"+t.tool.get("name")+" \n Dataset:"+t.config.get_value("name")+' \n Region(s):\n \n ',n=function(){Galaxy.modal.hide(),e(window).unbind("keypress.check_enter_esc")},a=function(){var i,n=e('select[name="regions"] option:selected').val(),a=new m.default.GenomeRegion({chrom:(void 0).view.chrom,start:(void 0).view.low,end:(void 0).view.high}),s=h.map(e(".bookmark"),function(t){return new m.default.GenomeRegion({from_str:e(t).children(".position").text()})});i="cur"===n?[a]:"bookmarks"===n?s:[a].concat(s),Galaxy.modal.hide(),window.top.location.href=Galaxy.root+"visualization/sweepster?"+e.param({dataset_id:t.dataset.id,hda_ldda:t.dataset.get("hda_ldda"),regions:JSON.stringify(new p.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:n,Yes:a}})}},R.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&R.prototype.can_draw.call(this)},build_container_div:function(){return e("").addClass("track").attr("id","track_"+this.id)},set_dataset:function(e){this.dataset=e,this.data_manager.set("dataset",e)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var t=this,i=!1,n=!1,a=e("
");e(t.container_div).hover(function(){t.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=e(t.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,t.min_height_px),t.max_height_px);e(t.tiles_div).css("height",a),t.visible_height_px=t.max_height_px===a?0:a,t.on_resize()}).bind("dragend",function(e,s){t.tile_cache.clear(),n=!1,i||a.hide(),t.config.set_value("height",t.visible_height_px),t.changed()}).appendTo(t.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof Q?"LabelTrack":this instanceof ee?"ReferenceTrack":this instanceof te?"LineTrack":this instanceof se?"ReadTrack":this instanceof ae?"VariantTrack":this instanceof Z?"CompositeTrack":this instanceof ne?"FeatureTrack":""},show_message:function(t){return this.tiles_div.remove(),e("").addClass("message").html(t).appendTo(this.content_div)},init:function(t){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=e("").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=e.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:t};return e.getJSON(this.dataset.url(),a,function(t){if(t&&"error"!==t&&"error"!==t.kind)"no converter"===t?(i.container_div.addClass("error"),i.show_message(L)):"no data"===t||void 0!==t.data&&(null===t.data||0===t.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===t?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),window.setTimeout(function(){i.init()},i.data_query_wait)):"data"!==t&&"data"!==t.status||(t.valid_chroms&&(i.valid_chroms=t.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,e.when.apply(e,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");t.message&&(a.append(e("").text("View error").click(function(){Galaxy.modal.show({title:(0,c.default)("Trackster Error"),body:"
"+t.message+"
",buttons:{Close:function(){Galaxy.modal.hide()}}})})),a.append(e("").text(" ")),a.append(e("").text("Try again").click(function(){i.init(!0)})))}}),this.update_icons(),n}},predraw_init:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(i&&void 0!==i.min&&void 0!==i.max){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_default_value("min_value",n),t.config.set_default_value("max_value",a),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},get_drawables:function(){return this}});var K=function(t,i,n){X.call(this,t,i,n);var a=this;if(o(a.container_div,a.drag_handle_class,".group",a),this.filters_manager=new T.default.FiltersManager(this,"filters"in n?n.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=n.tool?new F(h.extend(n.tool,{track:this,tool_state:n.tool_state})):null,this.tile_cache=new m.default.Cache(10),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var s=new q({model:this.tool});s.render(),this.dynamic_tool_div=s.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=e("").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=e("").addClass("overlay").appendTo(this.content_div),n.mode&&this.change_mode(n.mode)};I(K.prototype,R.prototype,X.prototype,{action_icons_def:X.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(t){e(".tooltip").remove(),t.slotters[t.view.resolution_px_b].max_rows*=2,t.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(e){var t=this.to_dict();I(t,{data_manager:this.data_manager});var i=new this.constructor(this.view,e,t);return i.change_mode(this.mode),i.enabled=this.enabled,i},set_filters_manager:function(e){this.filters_manager=e,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var t=this;return e.getJSON(t.dataset.url(),{data_type:"data",stats:!0,chrom:t.view.chrom,low:0,high:t.view.max_high,hda_ldda:t.dataset.get("hda_ldda")},function(e){var i=e.data;if(isNaN(parseFloat(t.config.get_value("min_value")))||isNaN(parseFloat(t.config.get_value("max_value")))){var n=i.min,a=i.max;n=Math.floor(Math.min(0,Math.max(n,i.mean-2*i.sd))),a=Math.ceil(Math.max(0,Math.min(a,i.mean+2*i.sd))),t.config.set_value("min_value",n),t.config.set_value("max_value",a)}})},change_mode:function(e){var t=this;return t.mode=e,t.config.set_value("mode",e),"Auto"===e&&this.data_manager.clear(),t.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+t.mode+")"),t},update_icons:function(){var e=this;e.action_icons.filters_icon.toggle(e.filters_available),e.action_icons.tools_icon.toggle(null!==e.tool),e.action_icons.param_space_viz_icon.toggle(null!==e.tool)},_gen_tile_cache_key:function(e,t){return e+"_"+t},request_draw:function(e){e&&e.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(e,this)},before_draw:function(){this.max_height_px=0},_draw:function(t){var i=this;if(this.can_draw()){var n=t&&t.clear_after,a=this.view.low,s=this.view.high,o=this.view.container.width(),r=this.view.resolution_px_b,l=1/r;this.is_overview&&(a=this.view.max_low,s=this.view.max_high,r=o/(this.view.max_high-this.view.max_low),l=1/r),this.before_draw(),this.tiles_div.children().addClass("remove");for(var d,c,u=Math.floor(400*l),f=Math.floor(a/u),p=[],_=[];f*u").text(d).make_text_editable({num_cols:12,on_finish:function(t){e(".tooltip").remove(),this.config.set_value(o,r(t,1)),i()},help_text:"Set "+s+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(e,t,i,n){var a=this;h.filter(e,function(e){return e instanceof J}).length>0?(this.max_height_px=0,h.each(e,function(e){e instanceof J||(e.html_elt.remove(),a.draw_helper(e.region,i,{force:!0,mode:"Coverage"}))}),this._add_yaxis_label("max")):(this.container_div.find(".yaxislabel").remove(),h.find(e,function(e){return e.has_icons})&&h.each(e,function(e){e.has_icons||e.html_elt.css("padding-top",20)}))},get_mode:function(e){return this.mode},update_auto_mode:function(e){},_get_drawables:function(){return[this]},draw_helper:function(t,i,n){var a=this;n||(n={});var s=n.force,o=n.mode||this.mode,r=1/i,l=this._get_drawables(),d=this._gen_tile_cache_key(i,t),c=s?void 0:this.tile_cache.get_elt(d);if(c)return function(e){return e&&"track"in e}(c)&&this.show_tile(c,i),c;if(!1===n.data_fetch)return null;var u=function(){var e=h.find(G,function(e){return e===o})?"Coverage":o,i=h.map(l,function(i){return i.data_manager.get_data(t,e,r,a.data_url_extra_params)});return a.view.reference_track&&i.push(a.view.reference_track.data_manager.get_data(t,o,r,a.view.reference_track.data_url_extra_params)),i},f=e.Deferred();return this.tile_cache.set_elt(d,f),e.when.apply(e,u()).then(function(){var s,o=u(),r=o;if(h.find(o,function(e){return y.default.is_deferred(e)}))return a.tile_cache.set_elt(d,void 0),void e.when(a.draw_helper(t,i,n)).then(function(e){f.resolve(e)});a.view.reference_track&&(s=a.view.reference_track.data_manager.subset_entry(o.pop(),t));var c=[],p=[];h.each(l,function(e,t){var n=r[t];"Auto"===e.mode&&(e.mode=e.get_mode(n),e.update_auto_mode(e.mode)),c.push(e.mode),p.push(e.get_canvas_height(n,e.mode,i,w))});var _,m=a.view.canvas_manager.new_canvas(),g=t.get("start"),v=t.get("end"),w=Math.ceil((v-g)*i)+a.left_offset,b=h.max(p);m.width=w,m.height=n.height||b;var x=m.getContext("2d");x.translate(a.left_offset,0),l.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),h.each(l,function(e,n){_=e.draw_tile(r[n],x,c[n],t,i,s)}),void 0!==_&&(a.tile_cache.set_elt(d,_),a.show_tile(_,i)),f.resolve(_)}),f},get_canvas_height:function(e,t,i,n){return this.visible_height_px},_draw_line_track_tile:function(e,t,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",h.max(h.map(e.data,function(e){return e[1]}))||0);var s=t.canvas;return new C.default.LinePainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new J(this,n,a,s,e.data)},draw_tile:function(e,t,i,n,a,s){},show_tile:function(e,t){var i=e.html_elt;e.predisplay_actions();var n=Math.round((e.low-(this.is_overview?this.view.max_low:this.view.low))*t);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(e){var t=this;return" - region=["+(void 0!==e?e.toString():"all")+"], parameters=["+h.values(t.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(e,t){return"Auto"===t||("Coverage"===t?"bigwig"===e.dataset_type:"bigwig"!==e.dataset_type&&"no_detail"!==e.extra_info)},can_subset:function(e){return!e.message&&"no_detail"!==e.extra_info&&("bigwig"!==e.dataset_type||e.data[1][0]-e.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var Q=function(e,t){X.call(this,e,t,{resize:!1,header:!1}),this.container_div.addClass("label-track")};I(Q.prototype,X.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(t){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),s=Math.floor(i.low/a)*a,o=this.view.container.width(),r=e("").addClass("label-container");s").addClass("pos-label").text(y.default.commatize(s)).css({left:l})),s+=a}this.content_div.children(":first").remove(),this.content_div.append(r)}});var Z=function(e,t,i){if(K.call(this,e,t,i),this.drawables=[],"drawables"in i){for(var n,a=0;athis.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}h.each(this.drawables,function(e){(e instanceof ne||e instanceof se)&&e.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};I(Z.prototype,K.prototype,{display_modes:G,build_config_params:function(){return h.union(R.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:(0,c.default)("Show individual tracks"),css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_group()}}].concat(K.prototype.action_icons_def),to_dict:N.prototype.to_dict,add_drawable:N.prototype.add_drawable,unpack_drawables:N.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var e=this.visible_height_px;h.each(this.drawables,function(t){t.visible_height_px=e}),X.prototype.on_resize.call(this)},change_mode:function(e){K.prototype.change_mode.call(this,e);for(var t=0;ts&&(s=o)}for(a=0;athis.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,s=K.prototype.draw_helper.call(this,e,t,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),s},can_subset:function(e){return!0},draw_tile:function(e,t,i,n,a){var s=this.data_manager.subset_entry(e,n),o=s.data,r=t.canvas;t.font=t.canvas.manager.default_font,t.textAlign="center";for(var l=0,d=o.length;l12e3?"Squish":"Pack"},get_canvas_height:function(e,t,i,n){if("Coverage"===t||"bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,e.data,t),s=new this.painter(null,null,null,this.config.to_key_value_dict(),t);return Math.max(this.min_height_px,s.get_required_height(a,n))},draw_tile:function(e,t,i,n,a,s,o){var r=this,l=t.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(e.data)for(var _=this.filters_manager.filters,m=0,g=e.data.length;m1){var r;if(0===this.container_div.find(".yaxislabel.variant").length&&(r=this.config.get_value("summary_height")/2,this.tiles_div.prepend(e("").text("Summary").addClass("yaxislabel variant top").css({"font-size":r+"px",top:(this.config.get_value("summary_height")-r)/2+"px"})),this.config.get_value("show_sample_data"))){var l=o.join(" ");this.tiles_div.prepend(e("").html(l).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}r=("Squish"===this.mode?5:10)+"px",e(this.tiles_div).find(".sample").css({"font-size":r,"line-height":r}),e(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var se=function(e,t,i){ne.call(this,e,t,i),this.painter=C.default.ReadPainter,this.update_icons()};I(se.prototype,R.prototype,K.prototype,ne.prototype,{build_config_params:function(){return h.union(R.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var oe={CompositeTrack:Z,DrawableGroup:V,DiagonalHeatmapTrack:ie,FeatureTrack:ne,LineTrack:te,ReadTrack:se,VariantTrack:ae,VcfTrack:ae},re=function(e,t,i){if("copy"in e)return e.copy(i);var n=e.obj_type;return n||(n=e.track_type),new oe[n](t,i,e)};t.default={TracksterView:H,DrawableGroup:V,LineTrack:te,FeatureTrack:ne,DiagonalHeatmapTrack:ie,ReadTrack:se,VariantTrack:ae,CompositeTrack:Z,object_from_template:re}}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(5),d=s(l),c=i(10),u=s(c),h=i(17),f=s(h),p=i(55),_=s(p),m=i(25),g=s(m),v=e.View.extend({initialize:function(e){var t=this;this.modal=parent.Galaxy.modal||new f.default.View,this.form=new _.default(d.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(e,i){var a=i.model.attributes,s="",o={},l=a.job_id;l?s=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(s=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),d.default.get({url:s,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),t._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),e.resolve()},error:function(t,s){var o=t&&t.err_msg||"Uncaught error.";401==s?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new u.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:(0,r.default)("Tool request failed"),body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",t),e.reject()}})},postchange:function(e,t){var i={tool_id:t.model.get("id"),tool_version:t.model.get("version"),inputs:n.extend(!0,{},t.data.create())};t.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),d.default.request({type:"POST",url:Galaxy.root+"api/tools/"+t.model.get("id")+"/build",data:i,success:function(i){t.update(i),t.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",t),e.reject()}})}},e)),this.deferred=this.form.deferred,this.setElement(""),this.$el.append(this.form.$el)},_customize:function(e){var t=this,i=e.model.attributes,n=new u.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:(0,r.default)("Execute"),cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),e.portlet.disable(),t.submit(i,function(){n.unwait(),e.portlet.enable()})}});if(i.buttons={execute:n},i.job_id&&i.job_remap){if("job_produced_collection_elements"===i.job_remap)var a="Replace elements in collection ?",s="The previous run of this tool failed. Use this option to replace the failed element(s) in the dataset collectio that were produced during the previous tool run.";else var a="Resume dependencies from this job ?",s="The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.";i.inputs.push({label:a,name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:s})}var o={};Galaxy.user.attributes.preferences&&"extra_user_preferences"in Galaxy.user.attributes.preferences&&(o=JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences)),"true"===("use_cached_job|use_cached_job_checkbox"in o&&o["use_cached_job|use_cached_job_checkbox"])&&i.inputs.push({label:"BETA: Attempt to re-use jobs with identical parameters ?",help:"This may skip executing jobs that you have already run",name:"use_cached_job",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["No",!1],["Yes",!0]]})},submit:function(e,t){var i=this,s={tool_id:e.id,tool_version:e.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(s))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(t&&t());if(e.action!==Galaxy.root+"tool_runner/index"){var o=n("").attr({action:e.action,method:e.method,enctype:e.enctype});return a.each(s.inputs,function(e,t){o.append(n("").attr({name:t,value:e}))}),o.hide().appendTo("body").submit().remove(),void(t&&t())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",s),d.default.request({type:"POST",url:Galaxy.root+"api/tools",data:s,success:function(e){if(t&&t(),i.$el.children().hide(),i.$el.append(i._templateSuccess(e)),e.jobs&&e.jobs.length>0){i.$el.append(n("",{id:"webhook-view"}));new g.default.WebhookView({type:"tool",toolId:s.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){t&&t(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var n=!1;if(e&&e.err_data){var a=i.form.data.matchResponse(e.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:(0,r.default)("Job submission failed"),body:i._templateError(s,e&&e.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(e){var t=this,i=e.inputs,n=-1,a=null;for(var s in i){var o=i[s],r=this.form.data.match(s),l=this.form.field_list[r],d=this.form.input_list[r];if(r&&d&&l){if(!d.optional&&null==o)return this.form.highlight(r),!1;if(l.validate){var c=function(){t.form.trigger("reset")},u=l.validate(c);if(!u.valid)return this.form.highlight(r,u.message),!1}if(o&&o.batch){var h=o.values.length,f=h>0&&o.values[0]&&o.values[0].src;if(f)if(null===a)a=f;else if(a!==f)return this.form.highlight(r,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===n)n=h;else if(n!==h)return this.form.highlight(r,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+h+" selection(s) while a previous field contains "+n+"."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",s=n("").addClass("donemessagelarge").append(n("").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(e.outputs,function(e){s.append(n("").addClass("messagerow").append(n("").text(e.hid+": "+e.name)))}),s.append(n("").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),s}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return n("").addClass("errormessagelarge").append(n("").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(t||""))).append(n("").text(JSON.stringify(e,null,4)))}});t.default={View:v}}).call(t,i(2),i(0),i(1))},,,function(e,t,i){"use strict";function n(e){i(88)}Object.defineProperty(t,"__esModule",{value:!0});var a=i(43),s=i.n(a);for(var o in a)"default"!==o&&function(e){i.d(t,e,function(){return a[e]})}(o);var r=i(136),l=i(23),d=n,c=Object(l.a)(s.a,r.a,r.b,!1,d,null,null);t.default=c.exports},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(6),l=o(r),d=i(3),c=(o(d),e.View.extend(l.default.LoggableMixin).extend({_logNamespace:"list",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=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$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",a.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.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?s.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$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)})}})),u=c.extend(l.default.mixin(l.default.SelectableViewMixin,l.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),l.default.SelectableViewMixin.initialize.call(this,e),l.default.DraggableViewMixin.initialize.call(this,e),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=c.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 c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n(''),i=e.model.toJSON();return a.each(e.templates.warnings,function(a){t.append(n(a(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(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){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:l.default.wrapTemplate(['
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