Merge pull request #2 from dannon/conditional_galaxycloudrunner

Conditional galaxycloudrunner

.travis.yml

@@ -6,15 +6,11 @@ env:
   - TOX_ENV=py34-lint
   - TOX_ENV=py27-lint
   - TOX_ENV=py27-unit
-  - TOX_ENV=qunit
   - TOX_ENV=py27-first_startup
   - TOX_ENV=py27-lint_docstring_include_list
 
 matrix:
   include:
-    - env: TOX_ENV=qunit
-      addons:
-        chrome: stable
     - env: TOX_ENV=py34-first_startup
       addons:
         &py3_addons
@@ -38,6 +34,27 @@ matrix:
       # No version of Python is available via virtualenv on OS X workers, see https://github.com/travis-ci/travis-ci/issues/2312
       language: generic
       env: TOX_ENV=py27-first_startup
+    - name: js-unit
+      language: node_js
+      node_js:
+          - 10
+      before_install:
+        - cd client
+      install:
+        - yarn
+        - yarn run build
+      script:
+        - yarn run test
+    - name: js-lint
+      language: node_js
+      node_js:
+          - 10
+      before_install:
+        - cd client
+      install:
+        - yarn
+      script:
+        - yarn run eslint
 
 before_install:
   # Workaround for https://github.com/travis-ci/travis-ci/issues/7940

Makefile

@@ -160,13 +160,11 @@ client-format: node-deps ## Reformat client code
 client-watch: node-deps ## A useful target for parallel development building.
 	cd client && yarn run watch
 
-_client-test-mocha:  ## Run mocha tests via karma
-	cd client && yarn run test-mocha
+client-test: node-deps  ## Run JS unit tests via Karma
+	cd client && yarn run test
 
-_client-test-qunit:  ## Run qunit tests via karma
-	cd client && yarn run test-qunit
-
-client-test: client _client-test-mocha _client-test-qunit ## Run JS unit tests via Karma
+client-eslint: node-deps  ## Run client linting
+	cd client && yarn run eslint
 
 client-test-watch: client ## Watch and run qunit tests on changes via Karma
 	cd client && yarn run test-watch

client/.eslintignore

@@ -0,0 +1,6 @@
+*.test.js
+galaxy/scripts/qunit
+galaxy/scripts/mocha
+galaxy/scripts/libs
+galaxy/scripts/nls
+galaxy/scripts/legacy

client/.eslintrc.js

@@ -0,0 +1,19 @@
+module.exports = {
+    extends: ["eslint:recommended", "plugin:vue/essential"], // airbnb-base, eventually
+    env: {
+        browser: true
+    },
+    parserOptions: { parser: "babel-eslint" },
+    plugins: ["html"],
+    rules: {
+        "no-console": "off",
+        "no-unused-vars": ["error", { args: "none" }],
+        // I'd love to turn on camelcase, but it's a big shift with tons of current errors.
+        // camelcase: [
+        //     "error",
+        //     {
+        //         properties: "always"
+        //     }
+        // ]
+    }
+};

client/galaxy/scripts/app/galaxy.js

@@ -149,10 +149,14 @@ GalaxyApp.prototype._initLogger = function _initLogger(loggerOptions) {
         // load any logging namespaces from localStorage if we can
         try {
             loggerOptions.consoleNamespaceWhitelist = localStorage.getItem(NAMESPACE_KEY).split(",");
-        } catch (storageErr) {}
+        } catch (storageErr) {
+            console.debug(storageErr);
+        }
         try {
             loggerOptions.consoleFlattenMessages = localStorage.getItem(FLATTEN_LOG_MESSAGES_KEY) == "true";
-        } catch (storageErr) {}
+        } catch (storageErr) {
+            console.debug(storageErr);
+        }
         console.log(loggerOptions.consoleFlattenMessages);
     }
 
@@ -233,7 +237,9 @@ GalaxyApp.prototype._setUpListeners = function _setUpListeners() {
         var data = options.data;
         try {
             data = JSON.parse(data);
-        } catch (err) {}
+        } catch (err) {
+            // data isn't JSON, skip.
+        }
 
         self.lastAjax = {
             url: location.href.slice(0, -1) + options.url,

client/galaxy/scripts/components/Alert.vue

@@ -1,8 +1,6 @@
 <template>
     <b-alert :variant="galaxyKwdToBootstrap" :show="showP" v-bind="$props">
-        <slot>
-            {{ message }}
-        </slot>
+        <slot> {{ message }} </slot>
     </b-alert>
 </template>
 

client/galaxy/scripts/components/Citations.vue

@@ -2,23 +2,24 @@
     <b-card>
         <h4 slot="header" class="mb-0">
             Citations
-            <b-button v-if="viewRender" @click="toggleViewRender" title="Show all in BibTeX format." class="citations-to-bibtex">
-                <i class="fa fa-pencil-square-o"></i>
-                Show BibTeX
+            <b-button
+                v-if="viewRender"
+                @click="toggleViewRender"
+                title="Show all in BibTeX format."
+                class="citations-to-bibtex"
+            >
+                <i class="fa fa-pencil-square-o"></i> Show BibTeX
             </b-button>
             <b-button v-else @click="toggleViewRender" title="Return to formatted citation list.">
-                <i class="fa fa-times"></i>
-                Hide BibTeX
+                <i class="fa fa-times"></i> Hide BibTeX
             </b-button>
         </h4>
         <div v-if="source === 'histories'" class="infomessage">
-            When writing up your analysis, remember to include all references that should be cited in order
-            to completely describe your work. Also, please remember to <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.
+            When writing up your analysis, remember to include all references that should be cited in order to
+            completely describe your work. Also, please remember to
+            <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.
         </div>
-        <span v-if="viewRender" class="citations-formatted">
-            <p v-html="formattedReferences">
-            </p>
-        </span>
+        <span v-if="viewRender" class="citations-formatted"> <p v-html="formattedReferences"></p> </span>
         <pre v-else>
             <code class="citations-bibtex">
                 {{ content }}
@@ -27,6 +28,7 @@
     </b-card>
 </template>
 <script>
+import _ from "underscore";
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 import * as bibtexParse from "libs/bibtexParse";

client/galaxy/scripts/components/DataDialog.vue

@@ -1,29 +1,28 @@
 <template>
     <b-modal class="data-dialog-modal" v-model="modalShow" :ok-only="true" ok-title="Close">
         <template slot="modal-header">
-            <h5 class="modal-title">{{modalTitle}}</h5>
             <b-input-group v-if="optionsShow">
-                <b-input v-model="filter" placeholder="Type to Search"/>
+                <b-input v-model="filter" placeholder="Type to Search" />
                 <b-input-group-append>
                     <b-btn :disabled="!filter" @click="filter = ''">Clear</b-btn>
                 </b-input-group-append>
             </b-input-group>
         </template>
-        <b-alert v-if="errorMessage" variant="danger" :show="errorShow">
-            {{ errorMessage }}
-        </b-alert>
+        <b-alert v-if="errorMessage" variant="danger" :show="errorShow"> {{ errorMessage }} </b-alert>
         <div v-else>
             <div v-if="optionsShow">
-                <b-table small hover
+                <b-table
+                    small
+                    hover
                     :items="items"
                     :fields="fields"
                     :filter="filter"
                     @row-clicked="clicked"
-                    @filtered="filtered">
+                    @filtered="filtered"
+                >
                     <template slot="name" slot-scope="data">
-                        <i v-if="data.item.history_content_type == 'dataset'" class="fa fa-file-o"/>
-                        <i v-else class="fa fa-copy"/>
-                        {{ data.item.hid }}: {{ data.value }}
+                        <i v-if="data.item.history_content_type == 'dataset'" class="fa fa-file-o" />
+                        <i v-else class="fa fa-copy" /> {{ data.item.hid }}: {{ data.value }}
                     </template>
                     <template slot="extension" slot-scope="data">
                         {{ data.value ? data.value : "-" }}
@@ -32,14 +31,9 @@
                         {{ data.value ? data.value.substring(0, 16).replace("T", " ") : "-" }}
                     </template>
                 </b-table>
-                <div v-if="nItems == 0">
-                    No search results found for: {{ this.filter }}.
-                </div>
-            </div>
-            <div v-else>
-                <span class="fa fa-spinner fa-spin"/>
-                <span>Please wait...</span>
+                <div v-if="nItems == 0">No search results found for: {{ this.filter }}.</div>
             </div>
+            <div v-else><span class="fa fa-spinner fa-spin" /> <span>Please wait...</span></div>
         </div>
     </b-modal>
 </template>
@@ -49,6 +43,7 @@ import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
+import { getGalaxyInstance } from "app";
 
 Vue.use(BootstrapVue);
 
@@ -59,15 +54,6 @@ export default {
             required: true
         }
     },
-    computed: {
-        modalTitle() {
-            if (this.errorMessage) {
-                return "Failed to load datasets";
-            } else if (!this.optionsShow) {
-                return "Loading datasets";
-            }
-        }
-    },
     data() {
         return {
             fields: {
@@ -106,6 +92,7 @@ export default {
             this.modalShow = false;
         },
         load: function() {
+            let Galaxy = getGalaxyInstance();
             this.historyId = Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;
             if (this.historyId) {
                 axios

client/galaxy/scripts/components/DisplayStructured.vue

@@ -1,16 +1,16 @@
 <template>
     <div>
+        <!-- eslint-disable-next-line vue/require-v-for-key -->
         <div v-for="error in errorMessages">
-            <div class="alert alert-danger" role="alert">
-                {{ error }}
-            </div>
-        </div>
-        <div v-html="historyTemplate">
+            <div class="alert alert-danger" role="alert">{{ error }}</div>
         </div>
+        <div v-html="historyTemplate"></div>
     </div>
 </template>
 
 <script>
+import $ from "jquery";
+import { getGalaxyInstance } from "app";
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 import HDAModel from "mvc/history/hda-model";
@@ -62,6 +62,7 @@ export default {
         },
         makeHistoryView: function(historyDict) {
             window.hdas = historyDict.map(hda => {
+                let Galaxy = getGalaxyInstance();
                 return new HDAListItemEdit.HDAListItemEdit({
                     model: new HDAModel.HistoryDatasetAssociation(hda),
                     el: $("#hda-" + hda.id),

client/galaxy/scripts/components/GalaxyLoader.vue

@@ -1,7 +1,9 @@
 <template>
-    <div class="galaxy-loader"
-         :class="[`galaxy-loader_${style}`, {'galaxy-loader_center': center}]"
-         :style="{transform: `scale(${size/100})`}">
+    <div
+        class="galaxy-loader"
+        :class="[`galaxy-loader_${style}`, { 'galaxy-loader_center': center }]"
+        :style="{ transform: `scale(${size / 100})` }"
+    >
         <div class="galaxy-loader_strip-1"></div>
         <div class="galaxy-loader_strip-2"></div>
         <div class="galaxy-loader_strip-3"></div>

client/galaxy/scripts/components/HistoryImport.vue

@@ -3,12 +3,8 @@
         <b-card title="Import a history from an archive">
             <b-alert :show="hasErrorMessage" variant="danger">{{ errorMessage }}</b-alert>
             <p>Please provide a Galaxy history export URL or a history file.</p>
-            <b-form-group label="Archived History URL">
-                <b-form-input type="url" v-model="sourceURL"/>
-            </b-form-group>
-            <b-form-group label="Archived History File">
-                <b-form-file v-model="sourceFile"/>
-            </b-form-group>
+            <b-form-group label="Archived History URL"> <b-form-input type="url" v-model="sourceURL" /> </b-form-group>
+            <b-form-group label="Archived History File"> <b-form-file v-model="sourceFile" /> </b-form-group>
             <b-button type="submit">Import history</b-button>
         </b-card>
     </b-form>

client/galaxy/scripts/components/HistoryView.vue

@@ -1,38 +1,47 @@
 <template>
     <div id="structured-history-view">
-        <div id="history-view-controls" class="clear"> 
+        <div id="history-view-controls" class="clear">
             <div class="float-left">
-                <span v-if="historyHistory['purged'] == false" >
-                    <span v-if="historyData.user_is_owner == false" >
+                <span v-if="historyHistory['purged'] == false">
+                    <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.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>
+                        <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>
+                    <button id="show-structure" class="btn btn-secondary" v-on:click="showStructure">
+                        Show structure
+                    </button>
                 </span>
             </div>
             <div class="float-right">
                 <button id="toggle-deleted" class="btn btn-secondary">Include deleted</button>
                 <button id="toggle-hidden" class="btn btn-secondary">Include hidden</button>
             </div>
         </div>
+        <!-- eslint-disable-next-line vue/require-v-for-key -->
         <div v-for="error in errorMessages">
-            <div class="alert alert-danger" role="alert">
-                {{ error }}
-            </div>
+            <div class="alert alert-danger" role="alert">{{ error }}</div>
         </div>
-        <div :id="'history-' + historyHistory['id']" class="history-panel unified-panel-body" style="overflow: auto;"></div>
+        <div
+            :id="'history-' + historyHistory['id']"
+            class="history-panel unified-panel-body"
+            style="overflow: auto;"
+        ></div>
     </div>
 </template>
 
 <script>
+import $ from "jquery";
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 import Vue from "vue";
 import DisplayStructure from "components/DisplayStructured.vue";
 import QueryStringParsing from "utils/query-string-parsing";
 import HistoryView from "mvc/history/history-view";
+import { getGalaxyInstance } from "app";
 
 export default {
     props: {
@@ -95,6 +104,7 @@ export default {
             });
         },
         showStructure: function() {
+            let Galaxy = getGalaxyInstance();
             let displayStructureInstance = Vue.extend(DisplayStructure),
                 mountView = document.createElement("div");
             Galaxy.page.center.display(mountView);

client/galaxy/scripts/components/Masthead/index.vue

@@ -37,7 +37,6 @@ export default {
 };
 </script>
 
-
 <style lang="scss">
 #masthead:empty {
     display: none;

client/galaxy/scripts/components/Message.vue

@@ -1,5 +1,5 @@
 <template>
-  <div v-if="message" :class="[status + 'message']">{{ message }}</div>
+    <div v-if="message" :class="[status + 'message']">{{ message }}</div>
 </template>
 
 <script>