Merge branch 'release_18.05' into dev

client/galaxy/scripts/components/HistoryView.vue

@@ -6,7 +6,7 @@
                     <span v-if="historyData.user_is_owner == false" >
                         <button id="import" class="btn btn-secondary">Import and start using history</button>
                     </span>
-                    <span v-if="historyData.history_is_current == false">
+                    <span v-if="historyData.user_is_owner && historyData.history_is_current == false">
                         <button id="switch-history" class="btn btn-secondary" v-on:click="switchHistory">Switch to this history</button>
                     </span>
                     <button id="show-structure" class="btn btn-secondary" v-on:click="showStructure">Show structure</button>

client/galaxy/scripts/mvc/history/history-contents.js

@@ -35,9 +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 */
-    urlRoot: `${Galaxy.root}api/histories`,
-
     /** complete api url */
     url: function() {
         return `${this.urlRoot}/${this.historyId}/contents`;
@@ -50,6 +47,7 @@ var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
         });
 
         options = options || {};
+        this.urlRoot = `${Galaxy.root}api/histories`;
         _super.prototype.initialize.call(this, models, options);
 
         this.history = options.history || null;

client/galaxy/scripts/mvc/tours.js

@@ -47,7 +47,7 @@ const TOURPAGE_TEMPLATE = `
             </a>
              - <%- tour.attributes.description || "No description given." %>
              <% _.each(tour.attributes.tags, function(tag) { %>
-                <span class="label label-primary sm-label-pad">
+                <span class="badge badge-primary">
                     <%- tag.charAt(0).toUpperCase() + tag.slice(1) %>
                 </span>
              <% }); %>

client/galaxy/style/scss/base.scss

@@ -1127,18 +1127,14 @@ div.odd_row {
 // Tool panel stuff
 
 // Extra label colors
-.label-beta {
+.badge-beta {
     @extend .badge-warning;
 }
 
-.label-new {
+.badge-new {
     @extend .badge-info;
 }
 
-.sm-label-pad {
-    margin-right: 2px;
-}
-
 span.toolParameterExpandableCollapsable {
     font-weight: bold;
     cursor: pointer;
@@ -1289,6 +1285,19 @@ a.action-button {
     vertical-align: middle;
 }
 
+.btn-xs {
+    // The 'new' bootstrap 4 btn-sm is about the same size as the old btn-xs,
+    // should serve as a replacement for anything expecting this.
+    @extend .btn-sm;
+}
+
+.btn-default {
+    // A hopefully temporary alias (as with above) to provide backwards
+    // compatibility for external stuff using .btn-default, which is now
+    // .btn-secondary.
+    @extend .btn-secondary;
+}
+
 //.action-button > * {
 //    vertical-align: middle;
 //}

lib/galaxy/jobs/handler.py

@@ -214,6 +214,9 @@ def __monitor(self):
                     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):

lib/galaxy/jobs/runners/slurm.py

@@ -3,7 +3,10 @@
 """
 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_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 @@ def _get_slurm_state():
                     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)

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

static/style/blue/base.css

@@ -1736,45 +1736,47 @@ button.btn-primary {
       box-shadow: 0 0 0 0.2rem rgba(37, 83, 123, 0.5); }
 
 .btn-secondary, input[type="submit"],
-button, .action-button, .menubutton {
+button, .action-button, .btn-default, .menubutton {
   color: #212529;
   background-color: #dee2e6;
   border-color: #dee2e6; }
   .btn-secondary:hover, input[type="submit"]:hover,
-  button:hover, .action-button:hover, .menubutton:hover {
+  button:hover, .action-button:hover, .btn-default:hover, .menubutton:hover {
     color: #212529;
     background-color: #c8cfd6;
     border-color: #c1c9d0; }
   .btn-secondary:focus, input[type="submit"]:focus,
-  button:focus, .action-button:focus, .menubutton:focus, .btn-secondary.focus, input.focus[type="submit"],
-  button.focus, .focus.action-button, .focus.menubutton {
+  button:focus, .action-button:focus, .btn-default:focus, .menubutton:focus, .btn-secondary.focus, input.focus[type="submit"],
+  button.focus, .focus.action-button, .focus.btn-default, .focus.menubutton {
     box-shadow: 0 0 0 0.2rem rgba(222, 226, 230, 0.5); }
   .btn-secondary.disabled, input.disabled[type="submit"],
-  button.disabled, .disabled.action-button, .disabled.menubutton, .btn-secondary:disabled, input[type="submit"]:disabled,
-  button:disabled, .action-button:disabled, .menubutton:disabled {
+  button.disabled, .disabled.action-button, .disabled.btn-default, .disabled.menubutton, .btn-secondary:disabled, input[type="submit"]:disabled,
+  button:disabled, .action-button:disabled, .btn-default:disabled, .menubutton:disabled {
     color: #212529;
     background-color: #dee2e6;
     border-color: #dee2e6; }
   .btn-secondary:not(:disabled):not(.disabled):active, input[type="submit"]:not(:disabled):not(.disabled):active,
-  button:not(:disabled):not(.disabled):active, .action-button:not(:disabled):not(.disabled):active, .menubutton:not(:disabled):not(.disabled):active, .btn-secondary:not(:disabled):not(.disabled).active, input[type="submit"]:not(:disabled):not(.disabled).active,
-  button:not(:disabled):not(.disabled).active, .action-button:not(:disabled):not(.disabled).active, .menubutton:not(:disabled):not(.disabled).active,
+  button:not(:disabled):not(.disabled):active, .action-button:not(:disabled):not(.disabled):active, .btn-default:not(:disabled):not(.disabled):active, .menubutton:not(:disabled):not(.disabled):active, .btn-secondary:not(:disabled):not(.disabled).active, input[type="submit"]:not(:disabled):not(.disabled).active,
+  button:not(:disabled):not(.disabled).active, .action-button:not(:disabled):not(.disabled).active, .btn-default:not(:disabled):not(.disabled).active, .menubutton:not(:disabled):not(.disabled).active,
   .show > .btn-secondary.dropdown-toggle,
   .show > input.dropdown-toggle[type="submit"],
   .show >
   button.dropdown-toggle,
   .show > .dropdown-toggle.action-button,
+  .show > .dropdown-toggle.btn-default,
   .show > .dropdown-toggle.menubutton {
     color: #212529;
     background-color: #c1c9d0;
     border-color: #bac2cb; }
     .btn-secondary:not(:disabled):not(.disabled):active:focus, input[type="submit"]:not(:disabled):not(.disabled):active:focus,
-    button:not(:disabled):not(.disabled):active:focus, .action-button:not(:disabled):not(.disabled):active:focus, .menubutton:not(:disabled):not(.disabled):active:focus, .btn-secondary:not(:disabled):not(.disabled).active:focus, input[type="submit"]:not(:disabled):not(.disabled).active:focus,
-    button:not(:disabled):not(.disabled).active:focus, .action-button:not(:disabled):not(.disabled).active:focus, .menubutton:not(:disabled):not(.disabled).active:focus,
+    button:not(:disabled):not(.disabled):active:focus, .action-button:not(:disabled):not(.disabled):active:focus, .btn-default:not(:disabled):not(.disabled):active:focus, .menubutton:not(:disabled):not(.disabled):active:focus, .btn-secondary:not(:disabled):not(.disabled).active:focus, input[type="submit"]:not(:disabled):not(.disabled).active:focus,
+    button:not(:disabled):not(.disabled).active:focus, .action-button:not(:disabled):not(.disabled).active:focus, .btn-default:not(:disabled):not(.disabled).active:focus, .menubutton:not(:disabled):not(.disabled).active:focus,
     .show > .btn-secondary.dropdown-toggle:focus,
     .show > input.dropdown-toggle[type="submit"]:focus,
     .show >
     button.dropdown-toggle:focus,
     .show > .dropdown-toggle.action-button:focus,
+    .show > .dropdown-toggle.btn-default:focus,
     .show > .dropdown-toggle.menubutton:focus {
       box-shadow: 0 0 0 0.2rem rgba(222, 226, 230, 0.5); }
 
@@ -2125,7 +2127,7 @@ button, .btn-group-lg > .action-button, .btn-group-lg > .menubutton {
   border-radius: 0.3rem; }
 
 .btn-sm, .btn-group-sm > .btn, .btn-group-sm > input[type="submit"], .btn-group-sm >
-button, .btn-group-sm > .action-button, .btn-group-sm > .menubutton, .multi-panel-history .control-column .btn, .multi-panel-history .control-column input[type="submit"], .multi-panel-history .control-column
+button, .btn-group-sm > .action-button, .btn-group-sm > .menubutton, .btn-xs, .multi-panel-history .control-column .btn, .multi-panel-history .control-column input[type="submit"], .multi-panel-history .control-column
 button, .multi-panel-history .control-column .action-button, .multi-panel-history .control-column .menubutton, .multi-panel-history .history-column .panel-controls .btn, .multi-panel-history .history-column .panel-controls input[type="submit"], .multi-panel-history .history-column .panel-controls
 button, .multi-panel-history .history-column .panel-controls .action-button, .multi-panel-history .history-column .panel-controls .menubutton {
   padding: 0.25rem 0.5rem;
@@ -2505,7 +2507,7 @@ button,
     margin-right: 0; }
 
 .btn-sm + .dropdown-toggle-split, .btn-group-sm > .btn + .dropdown-toggle-split, .btn-group-sm > input[type="submit"] + .dropdown-toggle-split, .btn-group-sm >
-button + .dropdown-toggle-split, .btn-group-sm > .action-button + .dropdown-toggle-split, .btn-group-sm > .menubutton + .dropdown-toggle-split, .multi-panel-history .control-column .btn + .dropdown-toggle-split, .multi-panel-history .control-column input[type="submit"] + .dropdown-toggle-split, .multi-panel-history .control-column
+button + .dropdown-toggle-split, .btn-group-sm > .action-button + .dropdown-toggle-split, .btn-group-sm > .menubutton + .dropdown-toggle-split, .btn-xs + .dropdown-toggle-split, .multi-panel-history .control-column .btn + .dropdown-toggle-split, .multi-panel-history .control-column input[type="submit"] + .dropdown-toggle-split, .multi-panel-history .control-column
 button + .dropdown-toggle-split, .multi-panel-history .control-column .action-button + .dropdown-toggle-split, .multi-panel-history .control-column .menubutton + .dropdown-toggle-split, .multi-panel-history .history-column .panel-controls .btn + .dropdown-toggle-split, .multi-panel-history .history-column .panel-controls input[type="submit"] + .dropdown-toggle-split, .multi-panel-history .history-column .panel-controls
 button + .dropdown-toggle-split, .multi-panel-history .history-column .panel-controls .action-button + .dropdown-toggle-split, .multi-panel-history .history-column .panel-controls .menubutton + .dropdown-toggle-split {
   padding-right: 0.375rem;
@@ -3715,18 +3717,18 @@ button .badge, .action-button .badge, .menubutton .badge {
     text-decoration: none;
     background-color: #198e19; }
 
-.badge-info, .label-new {
+.badge-info, .badge-new {
   color: #fff;
   background-color: #1cbceb; }
-  .badge-info[href]:hover, [href].label-new:hover, .badge-info[href]:focus, [href].label-new:focus {
+  .badge-info[href]:hover, [href].badge-new:hover, .badge-info[href]:focus, [href].badge-new:focus {
     color: #fff;
     text-decoration: none;
     background-color: #119ac3; }
 
-.badge-warning, .label-beta {
+.badge-warning, .badge-beta {
   color: #212529;
   background-color: #f69713; }
-  .badge-warning[href]:hover, [href].label-beta:hover, .badge-warning[href]:focus, [href].label-beta:focus {
+  .badge-warning[href]:hover, [href].badge-beta:hover, .badge-warning[href]:focus, [href].badge-beta:focus {
     color: #212529;
     text-decoration: none;
     background-color: #ce7b08; }
@@ -9003,7 +9005,7 @@ button, .action-button, .menubutton {
   white-space: normal; }
 
 .btn-secondary, input[type="submit"],
-button, .action-button, .menubutton {
+button, .action-button, .btn-default, .menubutton {
   border: 1px solid #bfbfbf; }
 
 .dropdown-menu {
@@ -13351,9 +13353,6 @@ div.odd_row {
 #footer {
   display: none; }
 
-.sm-label-pad {
-  margin-right: 2px; }
-
 span.toolParameterExpandableCollapsable {
   font-weight: bold;
   cursor: pointer; }