epiviz · dependabot · Sep 25, 2018 · Sep 25, 2018 · Sep 25, 2018 · Feb 4, 2019
diff --git a/data-provider/index.html b/data-provider/index.html
@@ -0,0 +1,13 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <meta http-equiv="Refresh" content="2; url=//epivizfileparser.readthedocs.io/en/latest/" />
+</head>
+
+<body>
+    <p>If the browser does not automatically redirect the page, Please click <a
+            href="//epivizfileparser.readthedocs.io/en/latest/">this link</a>.</p>
+</body>
+
+</html>
diff --git a/index.html b/index.html
@@ -230,7 +230,11 @@ <h3>Publications</h3>
 
     <div class="row">
         <ul>
-
+            <li>Kancherla J, Zhang A, Gottfried B and Bravo HC. (2018) Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets.
+                <a href="https://dx.doi.org/10.12688/f1000research.15433.1">F1000 Research</a>
+            </li>
+
+
             <li>Wagner, J., Chelaru, F., Kancherla, J., Paulson, JN., Felix, V., Mahurkar, A., Corrada Bravo, H. (2018). “Metaviz: interactive statistical and visual analysis of metagenomic data”.
                 <a href="https://doi.org/10.1093/nar/gky136">Nucleic Acids Research</a>
             </li>

diff --git a/polymer-old/charts/components/font-roboto/package-lock.json b/polymer-old/charts/components/font-roboto/package-lock.json
diff --git a/polymer-old/charts/components/font-roboto/package.json b/polymer-old/charts/components/font-roboto/package.json
@@ -18,7 +18,7 @@
   "homepage": "https://github.com/PolymerElements/font-roboto/",
   "devDependencies": {
     "@polymer/gen-typescript-declarations": "^1.1.1",
-    "bower": "^1.8.0"
+    "bower": "^1.8.8"
   },
   "scripts": {
     "update-types": "bower install && gen-typescript-declarations --deleteExisting --outDir ."

diff --git a/post/2019-02-04-epiviz-fileserver/bower_components/epiviz-charts/.eslintrc.json b/post/2019-02-04-epiviz-fileserver/bower_components/epiviz-charts/.eslintrc.json
@@ -0,0 +1,19 @@
+{
+  "extends": ["eslint:recommended", "google"],
+  "parserOptions": {
+    "ecmaVersion": 6
+  },
+  "env": {
+    "browser": true
+  },
+  "plugins": ["html"],
+  "rules": {
+    "brace-style": "off",
+    "new-cap": ["error", { "capIsNewExceptions": ["Polymer"] }],
+    "no-var": "off",
+    "require-jsdoc": "off"
+  },
+  "globals": {
+    "Polymer": true
+  }
+}
diff --git a/post/2019-02-04-epiviz-fileserver/bower_components/epiviz-charts/.gitignore b/post/2019-02-04-epiviz-fileserver/bower_components/epiviz-charts/.gitignore
@@ -0,0 +1,7 @@
+bower_components/
+node_modules/
+.vscode/
+data__
+performance/node_modules/
+performane/screenshots/
+.DS_Store
diff --git a/post/2019-02-04-epiviz-fileserver/bower_components/epiviz-charts/README.md b/post/2019-02-04-epiviz-fileserver/bower_components/epiviz-charts/README.md
@@ -0,0 +1,71 @@
+# Installation
+
+`bower install epiviz/epiviz-chart`
+
+# Documentation
+
+run a local instance of polymer-server
+`polymer serve`
+
+Then navigate to http://localhost:8080/components/epiviz-chart/
+
+# Demo
+
+run a local instance of polymer-server
+`polymer serve`
+
+Then navigate to http://localhost:8080/components/epiviz-chart/demo/
+
+
+# Update chartSettings:
+
+```
+# get chart
+chart = document.querySelector("#chart1");
+# get current chart settings
+currentSettings = chart.ChartSettings;
+# modify chart settings
+...
+
+# set settings back to chart
+chart.setAttribute("chart-settings", JSON.stringify(currentSettings));
+```
+
+# Epiviz-environment
+
+### must use polymer api to add charts to environment. Js dom api does not properly initialize elements
+
+for example
+
+if the page contains
+
+```
+<epiviz-environment id="env">
+</epiviz-environment>
+```
+
+to add an epiviz chart for example line-track.
+
+# create a new element
+```
+elem = document.createElement('epiviz-scatter-plot'); 
+elem.dimS = ['affy1', 'affy2']; 
+elem.className="charts"
+```
+
+# query dom for environment
+`ot = document.querySelector('#env')`
+
+# add chart
+`Polymer.dom(ot).appendChild(elem)`
+
+
+# Optimize elements for productions. 
+```
+npm install -g polymer-bundler
+
+polymer-bundler --inline-scripts --inline-css --strip-comments epiviz-charts.html > dist/epiviz-charts.html
+```
+
+
+