Merge branch 'release_18.05' into dev

.ci/jenkins/selenium/run_tests.sh

@@ -17,12 +17,18 @@ fi
 mkdir -p "$GALAXY_TEST_ERRORS_DIRECTORY"
 mkdir -p "$GALAXY_TEST_SCREENSHOTS_DIRECTORY"
 
-# /etc/passwd hack needed as long as make client requires git.
-# https://github.com/galaxyproject/galaxy/issues/5912
-docker run -v /etc/passwd:/etc/passwd -v `pwd`:`pwd`:rw -w `pwd` -u $UID $GALAXY_TEST_CLIENT_BUILD_IMAGE /bin/bash -c 'make client-production-maps'
+mkdir -p ~/.jenkins-yarn-cache
+YARN_CACHE_FOLDER=~/.jenkins-yarn-cache
+
+# Set git environment variables to enable Git. https://github.com/galaxyproject/galaxy/issues/5912
+# Setup volume and environment variable to cache this users yarn build.
+docker run -e GIT_COMMITTER_NAME=Jenkins -e GIT_COMMITTER_EMAIL=jenkins@galaxyproject.org \
+           -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER:rw \
+           -v `pwd`:`pwd`:rw -w `pwd` -u $UID $GALAXY_TEST_CLIENT_BUILD_IMAGE \
+           /bin/bash -c 'make client-production-maps'
 
 # Start Selenium server in the test Docker container.
-DOCKER_RUN_EXTRA_ARGS="-e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY} ${DOCKER_RUN_EXTRA_ARGS}"
+DOCKER_RUN_EXTRA_ARGS="-v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY} ${DOCKER_RUN_EXTRA_ARGS}"
 export DOCKER_RUN_EXTRA_ARGS
 
 ./run_tests.sh --dockerize --db postgres --external_tmp --clean_pyc --skip_flakey_fails --selenium "$@"

client/galaxy/scripts/components/RuleCollectionBuilder.vue

@@ -202,11 +202,11 @@
                                     :multiple="mappingTargets()[map.type].multiple"
                                     :ordered="true"
                                     :value-as-list="true">
-                                    <span v-b-tooltip.hover.focus :title="titleRemoveMapping" class="fa fa-times" @click="removeMapping(map.index)"></span>
+                                    <span v-b-tooltip.hover :title="titleRemoveMapping" class="fa fa-times" @click="removeMapping(map.index)"></span>
                                 </column-selector>
                             </div>
                             <div class="buttons rule-edit-buttons d-flex justify-content-end">
-                                <button v-b-tooltip.hover.focus :title="titleAddColumnDefinition" type="button" class="dropdown-toggle btn btn-primary mr-1" data-toggle="dropdown" v-if="unmappedTargets.length > 0">
+                                <button v-b-tooltip.hover :title="titleAddColumnDefinition" type="button" class="dropdown-toggle btn btn-primary mr-1" data-toggle="dropdown" v-if="unmappedTargets.length > 0">
                                     <span class="fa fa-plus rule-add-mapping"></span> {{ "Add Definition" }}<span class="caret"></span>
                                 </button>
                                 <div class="dropdown-menu" role="menu">
@@ -220,7 +220,7 @@
                                       {{ mappingTargets()[target].label }}
                                     </a>
                                 </div>
-                                <b-button v-b-tooltip.hover.focus.bottom :title="titleApplyColumnDefinitions" class="rule-mapping-ok" v-if="!hasActiveMappingEdit" @click="displayRuleType = null">{{ l("Apply") }}</b-button>
+                                <b-button v-b-tooltip.hover.bottom :title="titleApplyColumnDefinitions" class="rule-mapping-ok" v-if="!hasActiveMappingEdit" @click="displayRuleType = null">{{ l("Apply") }}</b-button>
                             </div>
                         </div>
                         <div class="rule-summary" v-if="displayRuleType == null">
@@ -256,7 +256,7 @@
                             </ol>
                             <div class="rules-buttons">
                                 <div class="btn-group dropup">
-                                  <button type="button" v-b-tooltip.hover.focus.bottom :title="titleRulesMenu" class="rule-menu-rules-button primary-button dropdown-toggle" data-toggle="dropdown">
+                                  <button type="button" v-b-tooltip.hover.bottom :title="titleRulesMenu" class="rule-menu-rules-button primary-button dropdown-toggle" data-toggle="dropdown">
                                     <span class="fa fa-plus"></span> {{ l("Rules") }}<span class="caret"></span>
                                   </button>
                                   <div class="dropdown-menu" role="menu">
@@ -268,7 +268,7 @@
                                   </div>
                                 </div>
                                 <div class="btn-group dropup">
-                                    <button type="button" v-b-tooltip.hover.focus.bottom :title="titleFilterMenu" class="rule-menu-filter-button primary-button dropdown-toggle" data-toggle="dropdown">
+                                    <button type="button" v-b-tooltip.hover.bottom :title="titleFilterMenu" class="rule-menu-filter-button primary-button dropdown-toggle" data-toggle="dropdown">
                                         <span class="fa fa-plus"></span> {{ l("Filter") }}<span class="caret"></span>
                                     </button>
                                     <div class="dropdown-menu" role="menu">
@@ -280,7 +280,7 @@
                                   </div>
                                 </div>
                                 <div class="btn-group dropup">
-                                    <button type="button" v-b-tooltip.hover.focus.bottom :title="titleColumMenu" class="rule-menu-column-button primary-button dropdown-toggle" data-toggle="dropdown">
+                                    <button type="button" v-b-tooltip.hover.bottom :title="titleColumMenu" class="rule-menu-column-button primary-button dropdown-toggle" data-toggle="dropdown">
                                         <span class="fa fa-plus"></span> {{ l("Column") }}<span class="caret"></span>
                                     </button>
                                     <div class="dropdown-menu" role="menu">
@@ -311,13 +311,13 @@
             </div>
         </rule-modal-middle>
         <rule-modal-footer v-if="ruleView == 'source'">
-            <b-button v-b-tooltip.hover.focus :title="titleSourceCancel" @click="cancelSourceEdit" class="rule-btn-cancel">
+            <b-button v-b-tooltip.hover :title="titleSourceCancel" @click="cancelSourceEdit" class="rule-btn-cancel">
                 {{ l("Cancel") }}
             </b-button>
-            <b-button v-b-tooltip.hover.focus :title="titleSourceReset" class="creator-reset-btn rule-btn-reset">
+            <b-button v-b-tooltip.hover :title="titleSourceReset" class="creator-reset-btn rule-btn-reset">
                 {{ l("Reset") }}
             </b-button>
-           <b-button v-b-tooltip.hover.focus :title="titleSourceApply" @click="attemptRulePreview" class="rule-btn-okay">
+           <b-button v-b-tooltip.hover :title="titleSourceApply" @click="attemptRulePreview" class="rule-btn-okay">
                 {{ l("Apply")}}
             </b-button>
         </rule-modal-footer>
@@ -345,20 +345,20 @@
                 </div>
                 <div class="rule-footer-name-group" v-if="showCollectionNameInput">
                     <b-input class="collection-name"
-                    :placeholder="namePlaceholder" :title="namePlaceholder" v-b-tooltip.hover.focus v-model="collectionName" />
+                    :placeholder="namePlaceholder" :title="namePlaceholder" v-b-tooltip.hover v-model="collectionName" />
                     <label>
                         {{ l("Name") }}:
                     </label>
                 </div>
             </div>
 
-            <b-button v-b-tooltip.hover.focus :help="titleCancel" @click="cancel" class="creator-cancel-btn rule-btn-cancel" tabindex="-1">
+            <b-button v-b-tooltip.hover :help="titleCancel" @click="cancel" class="creator-cancel-btn rule-btn-cancel" tabindex="-1">
                 {{ l("Cancel") }}
             </b-button>
-            <b-button v-b-tooltip.hover.focus @click="resetRulesAndState" :title="titleReset" class="creator-reset-btn rule-btn-reset">
+            <b-button v-b-tooltip.hover @click="resetRulesAndState" :title="titleReset" class="creator-reset-btn rule-btn-reset">
                 {{ l("Reset") }}
             </b-button>
-            <b-button v-b-tooltip.hover.focus @click="createCollection" :title="titleFinish" class="create-collection rule-btn-okay" variant="primary" :disabled="!validInput">
+            <b-button v-b-tooltip.hover @click="createCollection" :title="titleFinish" class="create-collection rule-btn-okay" variant="primary" :disabled="!validInput">
                 {{ finishButtonTitle }}
             </b-button>
         </rule-modal-footer>
@@ -382,10 +382,10 @@
             <p class="errormessagelarge">{{ errorMessage }}</p>
         </rule-modal-middle>
         <rule-modal-footer>
-            <b-button v-b-tooltip.hover.focus :title="titleCancel" @click="cancel" class="creator-cancel-btn" tabindex="-1">
+            <b-button v-b-tooltip.hover :title="titleCancel" @click="cancel" class="creator-cancel-btn" tabindex="-1">
                 {{ l("Close") }}
             </b-button>
-            <b-button v-b-tooltip.hover.focus :title="titleErrorOkay" @click="state = 'build'" tabindex="-1">
+            <b-button v-b-tooltip.hover :title="titleErrorOkay" @click="state = 'build'" tabindex="-1">
                 {{ l("Okay") }}
             </b-button>
         </rule-modal-footer>
@@ -583,7 +583,7 @@ const RegularExpressionInput = {
         <div>
             <label for="regular_expression" v-b-tooltip.hover :title="title">{{ label }}</label>
             <span v-b-popover.html="popoverContent" :title="popoverTitle" class="fa fa-question"></span>
-            <input v-b-tooltip.hover.focus.left :title="title" name="regular_expression" class="rule-regular-expression" type="text" :value="target" @input="$emit('update:target', $event.target.value)" />
+            <input v-b-tooltip.hover.left :title="title" name="regular_expression" class="rule-regular-expression" type="text" :value="target" @input="$emit('update:target', $event.target.value)" />
         </div>
     `,
     props: {
@@ -1537,6 +1537,7 @@ export default {
                                 subcollection[subElementProp] = childCollectionElements;
                                 subcollection.collection_type = collectionTypeAtDepth;
                                 elementsAtDepth = childCollectionElements;
+                                identifiersAtDepth = identifiersAtDepth[identifier];
                             }
                         }
                     }

client/galaxy/scripts/mvc/rules/rule-definitions.js

@@ -36,12 +36,11 @@ const applyRegex = function(regex, target, data, replacement, groupCount) {
     function newRow(row) {
         const source = row[target];
         const match = regExp.exec(source);
+        if (!match) {
+            failedCount++;
+            return null;
+        }
         if (!replacement) {
-            const match = regExp.exec(source);
-            if (!match) {
-                failedCount++;
-                return null;
-            }
             groupCount = groupCount && parseInt(groupCount);
             if (groupCount) {
                 if (match.length != groupCount + 1) {

client/galaxy/scripts/mvc/visualization/chart/utilities/series.js

@@ -1,4 +1,5 @@
 import * as _ from "underscore";
+import * as d3 from "d3";
 
 // TODO: This d3 must(?) just be global because various charts use different
 // versions, and we want to use whichever one that is.  I think.  I hope.

client/package.json

@@ -16,7 +16,7 @@
     "axios": "^0.17.0",
     "backbone": "1.3",
     "bibtex-parse-js": "^0.0.24",
-    "bootstrap": "^4.1.0",
+    "bootstrap": "^4.1.1",
     "bootstrap-tour": "https://github.com/sorich87/bootstrap-tour.git#6a1028fb562f9aa68c451f0901f8cfeb43cad140",
     "bootstrap-vue": "^2.0.0-rc.8",
     "d3": "3",
@@ -95,8 +95,8 @@
     "karma-polyfill": "^1.0.0",
     "karma-qunit": "^1.2.1",
     "karma-webpack": "^2.0.6",
-    "node-sass": "^4.8.3",
     "mocha": "^5.0.5",
+    "node-sass": "^4.8.3",
     "phantomjs-polyfill": "0.0.2",
     "phantomjs-prebuilt": "^2.1.7",
     "prettier": "^1.11.1",

client/yarn.lock

@@ -1411,10 +1411,14 @@ bootstrap@>=4.0.0-beta:
   version "4.0.0"
   resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-4.0.0.tgz#ceb03842c145fcc1b9b4e15da2a05656ba68469a"
 
-bootstrap@^4.0.0, bootstrap@^4.1.0:
+bootstrap@^4.0.0:
   version "4.1.0"
   resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-4.1.0.tgz#110b05c31a236d56dbc9adcda6dd16f53738a28a"
 
+bootstrap@^4.1.1:
+  version "4.1.1"
+  resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-4.1.1.tgz#3aec85000fa619085da8d2e4983dfd67cf2114cb"
+
 boxen@^0.5.1:
   version "0.5.1"
   resolved "https://registry.yarnpkg.com/boxen/-/boxen-0.5.1.tgz#5b73d8840eb7f3c8a155cbf69ed3ed68d4720014"

config/plugins/visualizations/heatmap/heatmap_default/src/script.js

@@ -9,7 +9,6 @@ var Series = window.bundleEntries.chartUtilities.Series;
 var Datasets = window.bundleEntries.chartUtilities.Datasets;
 var Jobs = window.bundleEntries.chartUtilities.Jobs;
 
-window.d3 = d3;
 var CommonWrapper = Backbone.View.extend({
     optionsDefault: {
         margin: {
@@ -495,8 +494,7 @@ _.extend(window.bundleEntries || {}, {
                 options.dataset_id = dataset.id;
                 options.dataset_groups = dataset_groups;
                 options.render = function(canvas_id, groups) {
-                    /* Where does HeatMap come from? It isn't in any local scope here. */
-                    new HeatMap({
+                    new CommonWrapper({
                         chart: options.chart,
                         canvas_id: canvas_id,
                         groups: groups

config/plugins/visualizations/jqplot/jqplot_bar/src/script.js

@@ -1,7 +1,8 @@
-import * as d3 from "d3";
+import * as d3 from 'd3';
 import jqplot from 'jqplot-exported/jqplot';
 import { LineRenderer } from 'jqplot-exported/LineRenderer';
 import { BarRenderer } from 'jqplot-exported/plugins/BarRenderer';
+import { OHLCRenderer } from 'jqplot-exported/plugins/OHLCRenderer';
 import { EnhancedLegendRenderer } from 'jqplot-exported/plugins/EnhancedLegendRenderer';
 
 var Series = window.bundleEntries.chartUtilities.Series;
@@ -230,17 +231,17 @@ _.extend(window.bundleEntries || {}, {
                     key   : group.get( 'key' )
                 });
             });
-            var plot = new Plot( {
+            var plot = new CommonWrapper( {
                 process             : options.process,
                 chart               : options.chart,
                 dataset_id          : dataset.id,
                 dataset_groups      : dataset_groups,
                 targets             : options.targets,
                 makeConfig          : function( groups, plot_config ){
-                    var boundary = Utilities.getDomains( groups, 'x' );
+                    var boundary = Series.getDomains( groups, 'x' );
                     $.extend( true, plot_config, {
                         seriesDefaults: {
-                            renderer: $.jqplot.OHLCRenderer,
+                            renderer: OHLCRenderer,
                             rendererOptions : {
                                 candleStick     : true,
                                 fillUpBody      : true,
@@ -264,7 +265,7 @@ _.extend(window.bundleEntries || {}, {
                     for ( var group_index in groups ) {
                         x_labels.push( groups[ group_index ].key );
                     }
-                    Utilities.mapCategories ( groups, x_labels );
+                    Series.mapCategories ( groups, x_labels );
                     return {
                         array: {
                             x : x_labels
@@ -332,11 +333,11 @@ _.extend(window.bundleEntries || {}, {
             options.dataset_groups = dataset_groups;
             options.makeConfig = function( groups, plot_config ){
                 $.extend( true, plot_config, {
-                    seriesDefaults: { renderer: $.jqplot.BarRenderer },
+                    seriesDefaults: { renderer: BarRenderer },
                     axes: { xaxis: { min : -1 }, yaxis: { pad : 1.2 } }
                 });
             };
-            new Plot( options );
+            new CommonWrapper( options );
         });
     },
     jqplot_line: function(options) {