Merging with dev

.gitignore

@@ -121,7 +121,7 @@ tool-data/shared/jars/
 sprite-*.less
 
 # JS, Local node_modules, and bower_components directories
-static/scripts/bundled
+static/scripts/bundled/[0-9]*
 node_modules
 bower_components
 

CONTRIBUTORS.md

@@ -6,14 +6,23 @@ The following individuals have contributed code to Galaxy:
 * Istvan Albert <istvan.albert@gmail.com>
 * Renato Alves <alves.rjc@gmail.com> <rjalves@igc.gulbenkian.pt>
 * Guruprasad Ananda <gua110@bx.psu.edu>
+* Evgeny Anatskiy <evgeny.anatskiy@gmail.com>
 * Florent Angly <florent.angly@gmail.com>
 * Raj Ayyampalayam <raj76@uga.edu>
+* Abdulrahman Azab <eng.azab@gmail.com>
 * Finn Bacall <finn.bacall@cs.man.ac.uk>
 * Dannon Baker <dannon.baker@gmail.com>
+* balto <balto_59@hotmail.fr>
 * Christopher Bare <christopherbare@gmail.com>
+* Bérénice Batut <berenice.batut@gmail.com>
 * Marius van den Beek <m.vandenbeek@gmail.com>
+* Maria Bernard <maria.bernard@jouy.inra.fr>
+* Jean-Frédéric Berthelot <jean-frederic.berthelot@lifl.fr>
+* Léo Biscassi <leo.biscassi@gmail.com>
 * Dan Blanchard <dan.blanchard@gmail.com>
+* Clemens Blank <blankclemens@gmail.com>
 * Daniel Blankenberg <dan.blankenberg@gmail.com> <dan@bx.psu.edu>
+* Jorrit Boekel <jorrit.boekel@scilifelab.se>
 * James Boocock <sfk2001@gmail.com>
 * Carlos Borroto <carlos.borroto@gmail.com>
 * Daniel Bouchard <dbouchard@corefacility.ca> <daniel.bouchard@phac-aspc.gc.ca>
@@ -26,6 +35,7 @@ The following individuals have contributed code to Galaxy:
 * Jennifer Cabral <jencabral@gmail.com>
 * Martin Čech <marten@bx.psu.edu>
 * Ramkrishna Chakrabarty <rc@bx.psu.edu>
+* Matt Chambers <matt.chambers42@gmail.com>
 * Brad Chapman <chapmanb@50mail.com>
 * John Chilton <jmchilton@gmail.com>
 * Saket Choudhary <saketkc@gmail.com>
@@ -43,13 +53,17 @@ The following individuals have contributed code to Galaxy:
 * Shane Dowling <shane@shanedowling.com>
 * John Duddy <jduddy@illumina.com>
 * Carl Eberhard <carlfeberhard@gmail.com>
+* Ignacio Eguinoa <ignacio.eguinoa@gmail.com>
 * Mark Einon <mark.einon@gmail.com>
 * Kyle Ellrott <kellrott@gmail.com> <kellrott@soe.ucsc.edu>
 * Eric Enns <eric.enns@gmail.com>
 * fescudie <fescudie@toulouse.inra.fr>
+* Anne Fouilloux <annefou@uio.no>
 * Dorine Francheteau <dorine@bx.psu.edu>
 * Jean-Frédéric (@JeanFred on Github)
+* Maximilian Friedersdorff <max@friedersdorff.com>
 * Jaime Frey <jfrey@cs.wisc.edu>
+* Ben Fulton <benmarkfulton@gmail.com>
 * Carrie Ganote <cganote@iu.edu>
 * Ryan Golhar <ngsbioinformatics@gmail.com>
 * Jeremy Goecks <jeremy.goecks@emory.edu> <jgoecks@gwu.edu>
@@ -63,29 +77,41 @@ The following individuals have contributed code to Galaxy:
 * Saskia Hiltemann <zazkia@gmail.com>
 * Rob Hooft <rob.hooft@nbic.nl>
 * Y. Hoogstrate <y.hoogstrate@erasmusmc.nl>
+* Hans-Rudolf Hotz <hrhotz@gmail.com>
 * Jian-Long Huang <jlh@pyhub.org>
 * Gert Hulselmans <gert.hulselmans@med.kuleuven.be>
+* Manabu Ishii <manabu.ishii.rb@gmail.com>
 * Jennifer Jackson <jen@bx.psu.edu>
 * Joachim Jacob <joachim.jacob@gmail.com>
+* Xiaoqian Jiang <jxq198409@hotmail.com>
 * Jim Johnson <jj@umn.edu> <jj@msi.umn.edu>
 * Radhesh Kamath <radhesh@bx.psu.edu>
+* Iyad Kandalaft <ik@iyadk.com>
 * Jan Kanis <jan.code@jankanis.nl>
 * David King <dcking@bx.psu.edu>
 * Rory Kirchner <roryk@mit.edu>
 * Edward Kirton <eskirton@lbl.gov>
+* Jasper Koehorst <jasperkoehorst@gmail.com>
+* Anup Kumar <anup.rulez@gmail.com>
 * Brad Langhorst <langhorst@neb.com>
+* Delphine Lariviere <lariviere.delphine@gmail.com>
 * Ross Lazarus <ross.lazarus@gmail.com> <rossl@bx.psu.edu>
+* Yvan Le Bras <yvan.le_bras@irisa.fr>
 * Gildas Le Corguillé @lecorguille
+* Alexander Lenail <alexander.lenail@tufts.edu>
 * Simone Leo <simone.leo@gmail.com>
 * Kanwei Li <kanwei@gmail.com>
 * Michael Li <michael.li@uwaterloo.ca>
 * Pierre Lindenbaum <plindenbaum@yahoo.fr>
 * Mikael Loaec <mikael.loaec@versailles.inra.fr>
+* Thoba Lose @thobalose
 * Philip Mabon <philipmabon@gmail.com>
 * Remi Marenco <remi.marenco@gmail.com> <remimarenco@gmail.com>
 * Zipho Mashologu <zipho@trustpay.biz>
 * Thomas McGowan <mcgo0092@msi.umn.edu>
 * Scott McManus <scottmcmanus@emory.edu> <scottmcmanus@gatech.edu>
+* Hervé Ménager <herve.menager@pasteur.fr>
+* Pablo Moreno <pablo.a.moreno@gmail.com>
 * Hunter Moseley <hunter.moseley@louisville.edu>
 * Takao Nakaguchi <takao.nakaguchi@gmail.com>
 * Arjun Nath <arjun@bx.psu.edu>
@@ -93,36 +119,48 @@ The following individuals have contributed code to Galaxy:
 * Eric Paniagua <paniagua.cshl@gmail.com>
 * Richard Park <rpark@bu.edu>
 * Lance Parsons <lparsons@princeton.edu>
+* Balthazar Pavot <balthazar.pavot@hotmail.fr>
 * Chinmay Rao <chinmay@bx.psu.edu>
 * Matt Ralston <mrals89@gmail.com>
+* ramezrawas <ramezrawas@gmail.com>
 * Eric Rasche <esr@tamu.edu> <rasche.eric@gmail.com> <rasche.eric@yandex.ru>
+* Athos Ribeiro <athoscr@fedoraproject.org>
 * Andrew Robinson <Andrew.Robinson@latrobe.edu.au>
+* Devon Ryan <dpryan79@gmail.com>
 * Michael Sauria <crockopotamus@gmail.com>
 * Andrea Sbardellati <andrea.sbardellati@crs4.it>
 * Ian Schenck <ian@bx.psu.edu>
 * Nick Semenkovich <semenko@alum.mit.edu>
+* Varun Shankar <varunshankar55@gmail.com>
 * Matthew Shirley <mdshw5@gmail.com>
+* Timur Shtatland <shtatland@neb.com>
 * Sourav Singh <ssouravsingh12@gmail.com>
 * Clare Sloggett <sloc@unimelb.edu.au>
 * Eteri Sokhoyan @Sokhoyan
 * Nicola Soranzo <nicola.soranzo@tgac.ac.uk> <nsoranzo@tiscali.it> <soranzo@crs4.it>
+* Nick Stoler <nick@nstoler.com>
 * Roy Storey <kiwiroy@gmail.com>
 * Hanfei Sun <ad9075@gmail.com>
 * Ilya Sytchev <hackdna@gmail.com>
+* Scott Szakonyi <sszakony@nd.edu>
 * James Taylor <james@jamestaylor.org>
 * Tomithy Too <tomithy.too@gmail.com>
 * David Trudgian <dave@trudgian.net> <david.trudgian@utsouthwestern.edu>
 * Nitesh Turaga <nitesh.turaga@gmail.com>
 * Clayton Turner <clayclay911@gmail.com>
 * Jesse c j van Dam <jesse.vandam@wur.nl>
+* Ashok Varadharajan <ashvark@gmail.com>
 * Marek Vavruša <marek@vavrusa.com>
 * Martijn Vermaat <m.vermaat.hg@lumc.nl>
 * Kelly Vincent <kpvincent@bx.psu.edu>
+* Jeremy Volkening <jdv@base2bio.com>
 * Greg Von Kuster <greg@bx.psu.edu>
 * Pavan Videm <videmp@informatik.uni-freiburg.de>
 * Hiral Vora <hvora1@uncc.edu>
+* Junzhou Wang <junzhouwang@gmail.com>
 * Andrew Warren <anwarren@vbi.vt.edu>
 * Trevor Wennblom <trevor@well.com>
+* Joachim Wolff <wolffj@informatik.uni-freiburg.de>
 * Thomas Wollmann <thomas.s.wollmann@gmail.com> <thomas.wollmann@bioquant.uni-heidelberg.de>
 * Jay Young <xiaojay@gmail.com>
 * Yi Zhang <yizhang@bx.psu.edu>

lib/galaxy/jobs/runners/kubernetes.py

@@ -3,6 +3,7 @@ Offload jobs to a Kubernetes cluster.
 """
 
 import logging
+import re
 from os import environ as os_environ
 
 from six import text_type
@@ -252,8 +253,12 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         return k8s_cont_image
 
     def __get_k8s_container_name(self, job_wrapper):
-        # TODO check if this is correct
-        return job_wrapper.job_destination.id
+        # These must follow a specific regex for Kubernetes.
+        raw_id = job_wrapper.job_destination.id
+        cleaned_id = re.sub("[^-a-z0-9]", "-", raw_id)
+        if cleaned_id.startswith("-") or cleaned_id.endswith("-"):
+            cleaned_id = "x%sx" % cleaned_id
+        return cleaned_id
 
     def check_watched_item(self, job_state):
         """Checks the state of a job already submitted on k8s. Job state is a AsynchronousJobState"""

lib/galaxy/webapps/tool_shed/api/repositories.py

@@ -1132,11 +1132,9 @@ class RepositoriesController( BaseAPIController ):
             os.remove( uploaded_file_name )
         if not ok:
             return {
-                "err_msg": message,
-                "content_alert": content_alert_str
+                "err_msg": message
             }
         else:
             return {
-                "message": message,
-                "content_alert": content_alert_str
+                "message": message
             }

static/scripts/bundled/admin.bundled.js

@@ -0,0 +1,2 @@
+webpackJsonp([4],{0:function(e,t,i){(function(e){var t=i(1),s=t,a=i(30).GalaxyApp,l=i(92),n=i(31);window.app=function(t,i){window.Galaxy=new a(t,i),Galaxy.debug("admin app"),Galaxy.params=Galaxy.config.params,s(function(){e.extend(t.config,{active_view:"admin"}),Galaxy.page=new n.View(e.extend(t,{Left:l}))})}}).call(t,i(2))},92:function(e,t,i){(function(t,s,a){var l=i(5),n=t.View.extend({initialize:function(e,i){var s=this;this.page=e,this.root=i.root,this.config=i.config,this.settings=i.settings,this.message=i.message,this.status=i.status,this.model=new t.Model({title:l("Administration")}),this.categories=new t.Collection([{title:"Server",items:[{title:"Data types registry",url:"admin/view_datatypes_registry"},{title:"Data tables registry",url:"admin/view_tool_data_tables"},{title:"Display applications",url:"admin/display_applications"},{title:"Manage jobs",url:"admin/jobs"}]},{title:"Tools and Tool Shed",items:[{title:"Search Tool Shed",url:"admin_toolshed/browse_tool_sheds",enabled:s.settings.is_tool_shed_installed},{title:"Search Tool Shed (Beta)",url:"admin_toolshed/browse_toolsheds",enabled:s.settings.is_tool_shed_installed&&s.config.enable_beta_ts_api_install},{title:"Monitor installing repositories",url:"admin_toolshed/monitor_repository_installation?installing_repository_ids="+s.settings.installing_repository_ids,enabled:s.settings.installing_repository_ids},{title:"Manage installed tools",url:"admin_toolshed/browse_repositories",enabled:s.settings.is_repo_installed},{title:"Reset metadata",url:"admin_toolshed/reset_metadata_on_selected_installed_repositories",enabled:s.settings.is_repo_installed},{title:"Download local tool",url:"admin/package_tool"},{title:"Tool lineage",url:"admin/tool_versions"},{title:"Reload a tool's configuration",url:"admin/reload_tool"},{title:"Review tool migration stages",url:"admin/review_tool_migration_stages"},{title:"View Tool Error Logs",url:"admin/tool_errors"},{title:"Manage Display Whitelist",url:"admin/sanitize_whitelist"},{title:"Manage Tool Dependencies",url:"admin/manage_tool_dependencies"}]},{title:"User Management",items:[{title:"Users",url:"admin/users"},{title:"Groups",url:"admin/groups"},{title:"Roles",url:"admin/roles"},{title:"API keys",url:"userskeys/all_users"},{title:"Impersonate a user",url:"admin/impersonate",enabled:s.config.allow_user_impersonation}]},{title:"Data",items:[{title:"Quotas",url:"admin/quotas",enabled:s.config.enable_quotas},{title:"Data libraries",url:"library_admin/browse_libraries"},{title:"Roles",url:"admin/roles"},{title:"Local data",url:"data_manager"}]},{title:"Form Definitions",items:[{title:"Form definitions",url:"forms/browse_form_definitions"}]},{title:"Sample Tracking",items:[{title:"Sequencers and external services",url:"external_service/browse_external_services"},{title:"Request types",url:"request_type/browse_request_types"},{title:"Sequencing requests",url:"requests_admin/browse_requests"},{title:"Find samples",url:"requests_common/find_samples?cntrller=requests_admin"}]}]),this.setElement(this._template())},render:function(){var e=this;this.$el.empty(),this.categories.each(function(t){var i=s(e._templateSection(t.attributes)),n=i.find(".ui-side-section-body");a.each(t.get("items"),function(t){(void 0===t.enabled||t.enabled)&&n.append(s("<div/>").addClass("ui-side-section-body-title").append(s("<a/>").attr({href:e.root+t.url,target:"galaxy_main"}).text(l(t.title))))}),e.$el.append(i)}),this.page.$("#galaxy_main").prop("src",this.root+"admin/center?message="+this.message+"&status="+this.status)},_templateSection:function(e){return["<div>",'<div class="ui-side-section-title">'+l(e.title)+"</div>",'<div class="ui-side-section-body"/>',"</div>"].join("")},_template:function(){return'<div class="ui-side-panel"/>'},toString:function(){return"adminPanel"}});e.exports=n}).call(t,i(3),i(1),i(2))}});
+//# sourceMappingURL=admin.bundled.js.map

test/galaxy_selenium/navigates_galaxy.py

@@ -449,7 +449,8 @@ class NavigatesGalaxy(HasDriver):
         self.click_xpath(self.navigation_data["selectors"]["masthead"]["workflow"])
 
     def click_button_new_workflow(self):
-        self.click_selector(self.navigation_data["selectors"]["workflows"]["new_button"])
+        element = self.wait_for_selector_clickable(self.navigation_data["selectors"]["workflows"]["new_button"])
+        element.click()
 
     def wait_for_sizzle_selector_clickable(self, selector):
         element = self._wait_on(