Merge from develop w/conflicts resolved

.gitignore

@@ -17,7 +17,9 @@ install.log
 .projectKnowledge
 nbproject
 static/dist
-my_narrative_env/
+my_narrative_venv/
+narrative_venv/
+new_narrative_env_2/
 
 # From https://github.com/github/gitignore/blob/master/Python.gitignore
 

.travis.yml

@@ -1,11 +1,13 @@
-sudo: false
+dist: trusty
+sudo: required
 language: python
 python:
   - "2.7"
 services:
   - docker
 addons:
   firefox: "latest"
+  chrome: stable
   apt:
     packages:
       - oracle-java8-installer

RELEASE_NOTES.md

@@ -3,6 +3,17 @@ The Narrative Interface allows users to craft KBase Narratives using a combinati
 
 This is built on the Jupyter Notebook v5.4.1 (more notes will follow).
 
+### Version 3.8.0
+- Generalized updates to support viewing the new version of the genome data type.
+- SCT-500 - Fix DomainAnnotation viewer widget.
+- SCT-380 - Updates to the RNA-Seq Volcano plot viewer.
+- KBASE-1916 - Fix data type descriptions in the Example tab of the data slideout.
+- SCT-923 - Improve Mycocosm public data search.
+- SCT-930 - Add a "show report" button to objects in the data panel.
+- Reformat and generalize the job logs for both the App Cell and standalone job log viewer widget.
+- Migrate unit tests to use HeadlessChrome and (optionally) Firefox.
+- Refactor Public Data in the Data Slideout to make use of the new KBase Search API.
+
 ### Version 3.7.2
 - SCT-908 - Fix formatting issues with heatmaps.
 - SCT-875 - Accept poorly formatted input data into the RNA-Seq data heatmap viewers.

bower.json

@@ -1,6 +1,6 @@
 {
   "name": "kbase-narrative",
-  "version": "3.7.2",
+  "version": "3.8.0",
   "homepage": "https://kbase.us",
   "dependencies": {
     "bluebird": "3.4.7",

kbase-extension/static/kbase/config/feature-config.json

@@ -3,5 +3,6 @@
     "jgiPublicStaging": true,
     "advanced": false,
     "developer": false,
-    "lazyWidgetRender": true
+    "lazyWidgetRender": true,
+    "batchAppMode": false
 }

kbase-extension/static/kbase/css/appCell.css

@@ -351,6 +351,17 @@ warning: orange
 
 */
 
+.btn.batch-active {
+    box-shadow: inset 0 3px 7px rgba(0, 0, 0, 0.125);
+    -webkit-box-shadow: inset 0 3px 7px rgba(0, 0, 0, 0.125);
+    background-color: #EEE;
+    border-color: #adadad;
+}
+
+.btn.batch-active:hover {
+    background-color: #CCC;
+}
+
 .btn.kb-app-cell-btn {
     color: rgb(33, 150, 243);
     background-color: #FFF;
@@ -378,7 +389,6 @@ warning: orange
     background-color: rgb(33, 150, 243);
 }
 
-
 /* Hovering over an active cell is different, it tries to make the tab look
    disassociated but using a gray background so it doesnt look like an inactive
    tab */

kbase-extension/static/kbase/css/batchMode.css

@@ -0,0 +1,4 @@
+.batch-mode-col{
+    padding: 5px 10px;
+    overflow: auto;
+}

kbase-extension/static/kbase/css/kbaseNarrative.css

@@ -74,7 +74,6 @@
 #kb-narr-name {
     font-family: Oxygen;
     font-weight: bold;
-    font-style: italic;
     font-size: 130%;
     padding-bottom: 7px;
     white-space: nowrap;
@@ -3177,7 +3176,6 @@ button.kb-data-obj {
 #kb-loading-blocker p {
     text-align: center;
     font-size: 24px;
-    font-family: Oxygen helvetica neue;
     font-weight: bold;
 }
 

kbase-extension/static/kbase/js/common/pythonInterop.js

@@ -76,6 +76,27 @@ define([], function () {
         return '\n' + indent + args.join(',\n' + indent) + '\n';
     }
 
+    function buildBatchAppRunner(cellId, runId, app, params) {
+        var paramSetName = 'batch_params',
+            pythonifiedParams = pythonifyValue(params, { autoIndent: true }),
+            positionalArgs = [
+                pythonifyValue(app.id),
+                paramSetName
+            ],
+            namedArgs = objectToNamedArgs({
+                tag: app.tag,
+                version: app.version,
+                cell_id: cellId,
+                run_id: runId
+            });
+        positionalArgs = positionalArgs.concat(namedArgs);
+        return [
+            paramSetName + ' = ' + pythonifiedParams,
+            'from biokbase.narrative.jobs.appmanager import AppManager',
+            'AppManager().run_app_batch(' + buildNiceArgsList(positionalArgs) + ')'
+        ].join('\n');
+    }
+
     function buildAppRunner(cellId, runId, app, params) {
         var positionalArgs = [
                 pythonifyValue(app.id),
@@ -217,6 +238,7 @@ define([], function () {
         objectToNamedArgs: objectToNamedArgs,
         pythonifyValue: pythonifyValue,
         buildAppRunner: buildAppRunner,
+        buildBatchAppRunner: buildBatchAppRunner,
         buildEditorRunner: buildEditorRunner,
         buildViewRunner: buildViewRunner,
         buildAdvancedViewRunner: buildAdvancedViewRunner,